I know it doesn't work well to glue after staining, but how about after pore
filling?

It will be an awful lot easier to fill and sand the parts before assembly,
but then I will be gluing some parts that have been poor filled. (african
mahogany)

I don't think it will matter since the water based material doesn't
penetrate much, and most of it will be sanded off, except what is in the
pores. So most of the surface will be clean for gluing.

Is this right, or am I asking for problems? Thanks.