This is a good way to perfect your speedy diaper changes, for sure! Consider it practice for when baby becomes mobile and you have to get that poop off ASAP before they flip over and crawl away!
A few things that might help for now, though:
I agree with swaddling on top, covering with a blanket, making sure the changing space is squishy soft, warm wipes...
My changing pad randomly has a built-in heating pad, which I never used with DD, but it gives me the idea that a warmed changing area might provide some comfort.
Make sure the lights are dim and the atmosphere mellow in general...
Sing, smile, and try to be generally pleasant and mellow. If you or DH are distressed then baby will pick up on that vibe.
If you're using cloth dipes, maybe forget about using a diaper cover (if this is relevant to your system), just to save some time when changing.
But my biggest suggestion is to try holding the baby over a potty every now and then to see if she eliminates that way. You can hold her in a position that's much more "natural" to her - sort of cradled and curled up. Maybe she'd respond well to that, as opposed to being laid on her back. Clean up time would also be less - just a quick wipe for a poop, but it wouldn't be smeared all over her bottom...
If she's really mad about being laid on her back, you could also do as much undressing/dressing as possible while holding the baby. Let her snuggle curled on your chest while you work off her pants or hike up her gown or whatever.