“What do you suppose that is in reference to?”
To both the earthly and Heavenly temples.
1 Kings 8:27
But will God indeed dwell on the earth? Behold, heaven and the heaven of heavens cannot contain You. How much less this temple which I have built!
Hebrews 8:5
[Levitical priests] who serve the copy and shadow of the heavenly things, as Moses was divinely instructed when he was about to make the tabernacle. For He said, “See that you make all things according to the pattern shown you on the mountain.”
I doubt you could produce a single Biblical Commentary, published by a reputable publisher, that would deny that references to God sitting between the Cherubim are references to the Mercy Seat on the Ark of the Covenant.
Take 1 Samuel 4:4, for example: “So the people sent to Shiloh, that they might bring from there the ark of the covenant of the Lord of hosts, who dwells between the cherubim. And the two sons of Eli, Hophni and Phinehas, were there with the ark of the covenant of God.”
And then 1 Chronicles 13:6:
“And David and all Israel went up to Baalah, to Kirjath Jearim, which belonged to Judah, to bring up from there the ark of God the Lord, who dwells between the cherubim, where His name is proclaimed.”
See the pattern?