Mogas is not the same as Avgas...not just composition, but testing, lot to lot, and by standard. 100 octane avgas is not the same as 100 octane auto fuel, and even among auto fuel of the same octane ratings, the fuel doesn't test out the same.
Autofuel, despite all the mythbusting wannabes who will tell you diferently, isn't stable. It doesn't last. It gums up, it goes rancid, and it's octane rating and properties change as it does so. If you're running fresh autofuel regularly through your low compression engine, you're probably okay...most of the time.
Autofuel lacks the aeromatics that preserve your fuel cells. Autofuel lacks a lot, really; it's only advantage in an aircraft is it's lower cost, and it can be false economy. Most mechanics are very much against the use of autofuel in aircraft...especially any mechanic that's had the privilege of gumming out carburetors and fuel systems that have been contaminated with auto fuel.
Replacing the carburetor with the same carburetor and jetting does not invalidate the STC, as it's an aircraft supplemental type certificate, not a carburetor STC. If the STC is issued inclusive of the same type carburetor, then changing for the same part number doesn't change the nature of efficacy of the STC.
You should check AD's for your aircraft and ensure that your carburetor does have the latest applicable float type (seems to be a revolving issue the last few years) before you install it, however.