When the altar is fully covered with block, the items rendering above the altar get really dark.

Screenshots:
Normal Runic Altar
Covered Runic Altar

I'm using Botania version r1.6-174 on the Regrowth pack version 0.7.4

It looks like a vanilla lighting issue, also, if you can't reproduce on the latest version (191 ATM) it is not a valid issue.

Here:
Normal Runic Altar
Covered Runic Altar

Also, I don't know if the colorless grass top is a vanilla bug or a Botania Bug.

I'm using Botania version r1.6-191.

The runic altar as a non-full block inherits its lighting from nearby blocks, further, you are completely obscuring the block space it is in, did you really expect that just because it renders things outside the block space that those items would remain lit?

TLDR; Vanilla bug, keep at least one side of the altar block space exposed to air.

It's a vanilla thing so not much we can do about it.