At the step of doing my basing. Question is do I need to put a protective cover(tape) over the bases before putting the matte finish spray on or will the PVA glue have no problems sticking to the matte finish?

you can just put a little tin foil over the basing... generally I'd protect the figure (and any painted base bits) first and then finish up with the basing finishing steps.

I spray the whole thing with Matt varnish (testors dull cote) then glue down flock/sand/static grass etc...never had any issues with it sticking to the varnish.