Wearing a 4¼-inch Commander in a holster made to fully cover a 5-inch gun is an expedient maneuver at best: It might 'save' some money on the short run, but you eventually get what you pay for (or not...).
If it simply must be done, then I would recommend trying a
Milt Sparks Summer Special. The 'original' design is not particularly closely molded, but it is nonetheless a very fine holster, and one of these in standard, 1911/Govt trim should 'fit' both of your pistols (albeit with obvious consequences, such as the end of the holster eventually collapsing around the Commander slide...).
Other than that, I think you will find really closely molded holsters a losing proposition in many cases, not just the obvious ones such as your SA dustcover issue. What you usually get is a holster that fits only the 'gun' it was molded to and none other. This, too, has obvious consequences, and I have come to prefer holsters that do
not look as if they were 'just painted on this morning.'
YMMV/HTH