Te'tzaveh, Shemos 29:42. Asher iva’eid lachem shama (the Mizbach Ha’olah.)

Rashi says that there is a machlokes whether the Shechina spoke to Moshe from above the Kapores of the Aron, or from the Mizbach ha’olah. (This is based on the last Braisoh in Maseches M’leches Hamishkon, but we have a girsa there that there are three shittos: Kappores, Mizbei’ach Hazohov, and Mizbei’ach Ho’oloh.) Reb Meir Simcha here says that this is the machlokes as to which kedusha is greater, that of a Beis Knesses (which mirrors the Mizbei'ach, because tefillos k’neged korbonos tiknum), or that of a Beis Medrash (the Aron Hakodesh, which contained the Luchos.) (He also talks about this in Hilchos Talmud Torah 1:2.)

(Also, see Rosh Hashonnoh 31a, where the Gemora says that the source of the voice of the Shechina changed with the deteriorating spiritual level of Klal Yisroel, initially from the Kapores, and changing until it finally emanated from the Midbar.)

But this is very hard to understand. There are psukim (Shemos 25:22 and Bamidbor 7:89) that unequivocally state that Hashem spoke to Moshe from the Kappores! What pressing need was there for Chazal to offer alternatives to the clear and straightforward meaning of the passuk?

The answer is that it is less important to know where Hashem is being mashreh His Shechina than to know how and where we, as individuals, will be able to perceive it. Hashra'as Hashechina may be more common than we realize, it may even be pervasive; it is we who are not receiving the signal. As Dante wrote, as translated by Jean Hollander in the new edition of The Paradiso,
The glory of Him Who moves all things
pervades the universe and shines
in one part more and in another less.
The Hashra'a, the potential, might be universal: the 'zohar,' however, requires a complete circuit, it needs proper reception to function. When Avraham asked Eliezer and Yishmael what they saw on Har Hamoriah, and they said they saw nothing, he told them "Shevu lachem poh im hachamor." If you, who grew in my household, don't see that the Shechina is on that mountain, then there is something wrong with your receiver-- you are 'Ahm hadomeh le'chamor.' And as Yaakov said as he woke from the dream of the Ladder, "Yeish Elokim bamakom hazeh...v'anochi lo yadati." So the question of "from whence issues the voice of Hashem?" is really a distraction, because the more important question is "where do we need to be in order to hear that voice." The answer to this question is, that some people learn how to hear God’s voice through tefilla– through their emotion and enthusiasm, and through mitzvos ma'asiyos, represented by the Mizbei'ach. Some people hear God’s voice through their limud hatorah, their rational faculty, represented by the Aron and the Luchos.

The pesukim that say that the voice emanated from atop the Kappores are stated in the singular and addressed specifically to Moshe Rabbeinu. Hashem spoke to Moshe Rabbeinu from atop the Luchos. Shemos 25:22- "ve'noaditi lecha sham vedibarti itcha...", and Bamidbor 7:89-Ube'vo Moshe...vayishma es hakol midabeir eilav...." But for the majority of the people, the "lachem" of our passuk, Hashem speaks to them through their Avodah, their mitzvos ma'asiyos, their tefilla.

Pascal once said that “Human beings must be known to be loved; but Divine beings must be loved to be known." (This is an interesting insight into the relationship between the word "da'as" and love; not only do we see this by Adam and Chava, Reb Moshe in his first Darash, in a drasha for Shabbos Hagadol, uses the same connection where Avraham said "Bamah eida ki irashena.") Chazal, lehavdil, are telling us that while it is true that some need to love Him in order to know Him, others need to know Him in order to love Him.

But it’s very important to realize that there has to be a complete Beis Hamikdosh. Nobody can know what it is to hear Hashem through pure reason; many philosophers have tried and failed; as the Arvei Nachal says in his criticism of pure reason in last week’s parsha and many other places. He says that “Knowing Hashem means knowing that you don’t know“ (umosar ha’adam min hab’heimah ayin.). Similarly, one can’t come to Hashem simply through emotion, because uninformed emotion is foolishness and walks in the forest and wild dances and all kinds of destructive delusion. A person with only one aspect is a cripple. (My father, HK'M, once told me that a young bochur came in to the Beis Medrash in Slabodkeh/Litteh, with the reputation that he knew Kodshim. Everyone was amazed, because Kodshim was reserved to mature talmidei chachomim. His chavrusa, Reb Leizer Platzinski, said, in five minutes I will tell you whether he deserves your hispailus: when you see a man walking on his hands, there are two alternative explanations: either he is an athlete or he is a cripple. If he can walk on his feet as well, he is an athlete. If he is walking on his hands because he can't walk on his feet normally, then he is a cripple and to be pitied. If this boy knows Nashim and Nezikin, then he's an illui. If he doesn't, then he's just abnormal.) You have to have a complete Beis Hamikdosh, with an Aron and a Mizbei’ach, you have to have a complete and healthy body with all its faculties. Then your relationship with Hashem might grow especially great in one respect and develp a primary focus on emotion or on mitzvos ma'asiyos or on reason.

As far as the Braisa we have, which says three shittos– Kappores, Mizbach ha’olah, and Mizbach Haketores – one might say that this reflects how different people most readily perceive holiness:
Some people hear the voice of God speaking through His Torah; Some people hear the voice of God through doing mitzvos maasi’os; Some people hear the voice of God through emotion. Respectively, these are the Aron, the Mizbach Ha’Olah, and the Mizbach HaKetores.
(I am reminded of what Gandhi once said; "There are people in the world so hungry, that God cannot appear to them except in the form of bread." Unfortunately, there is no shittah that the Shechinah spoke from the Shulchan. But the idea is certainly relevant, that it is through something that a person most thirsts for that he can perceive God, which is, to some extent, connected to Pascal’s idea.)

N.B.
1. Contrary to the assertion of a pestiferous anonymous correspondent, quoting Pascal (and Dante)does not make me Catholic, quoting Gandhi does not make me a Hindu, and quoting both of them does not make me Gil Student, and indeed the latter would not be so hideous a fate.

2. Others have said teirutzim on this kashe, all wonderful, but, to my mind, ranging from the interesting to the obscure to the byzantine. I strongly encourage you to look at the other teirutzim, and to decide which teretz is best supported by the pesukim themselves and least requires suspension of disbelief.