wood window paint

In my 100 yr old unfinished attic the wood sash or window is in dire need of replacement (quite disappointed over the built to last quality<G>). My attempted repair turned into a replacement(rotten wood). Anyway I'm building the new wood sash with milled 1 1/4" fir with bridle joints and expect to glaze the window with traditional putty
Should I prime and/or paint the fillet or under the glass? Somewhere or sometime I thought I read not to finish the fillet although I have no idea as to the why not. The existing window, as are all of the others in the house are bare wood albeit all are mostly original.
The existing window is 66" by 17" with 2 muntins...will I burn in "old house hell" if I use a larger single pane and use 2 surface mounted dividers? The attic is not readily accessible and from the street I don't think it would be noticeable.
Thanks Rod
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