Leave the feeder over the frames. . They will feed longer at night as the cluster doesn't have to move into the isolated section.
Pardon my ignorance, but what does this mean exactly. I know you're responding to the OP with regard to using an inner cover with a hive-top feeder, but I'm not sure what you mean by your last sentence.
The reason I ask is that I just pulled off two Mann Lake feeders and had to deal with lots of drone brood built into the feeders. I thought I'd cover the bottom of the feeders with 1/4" ply and build it in such a way as to keep 1 cm space up to the access holes in the feeder. However, I'm inferring from your post that the space between the frames and the feeder allows the cluster to keep warm at night AND access the feeder...meaning I just need to be better about clearing comb out of the feeder. Am I right, or did I read that wrong?
Sorry for the hijack...