Yep. Both of these are a side-effect of the gimmick method used to fake the higher-quality stuff.
The first one is probably fixable? Depends very heavily on if there's a on_upgrade_entity or whatever.
The second one is only fixable if I un-hide the new entities, but that causes problems with mod integrations (to be specific: infinite quality tiers, you'll be scrolling through 255 times the number of assembling machines - in SA that's AM1, AM2, AM3, EM plant, biochamber, foundry, and cryoplant.)