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It probably doesn't matter much either way. I left that little glass bridge in there for the minimal framing/added support it provides. (It does complete a support 'line' from the back to front of the sump.) If I run a refugium then it also serves to separate settled detritus from the return area and the refugium, although I suppose this makes cleaning ever so slightly harder as well.
As for the silicone gaps, I didn't worry about them. They are inevitable and haven't been a problem since my tank has been running.
If you run a refugium, aren’t you going to put a wall to separate the clarisea with the refugium?