I said barbs earlier mostly because I believe they make a better seal with the tubing than a smooth tube, of course either would work and tube is obviously simpler.
As for holes used to connect the top to the base, assuming an o-ring is being used to seal the connection, wiping the holes with solvent after drilling should not be any problem. The holes should be over-sized enough anyways to allow the screws to fit through easily as well as account for the screws moving a bit due to the different thermal expansion of the top/bottom.
If you really want to use brass fittings with a plastic top, I don't see that we're going to come to any good solution to it. Perhaps coat the threads with solvent and while it is fluid screw the fitting into place - the plastic should harden into shape following the threads while sealing any microcracks, then if needed remove the fitting (it shouldn't actually be glued in unlike using a plastic fitting as well) and apply your favorite thread sealer eg. teflon tape.
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