I'm no expert, but for what the ECU does, I don't think it makes a difference on the transmission. If you want to verify this quickly, do a search for the ATX to MTX conversion threads. Look for mention of the ECU there. If nobody else is changing the ECU going from ATX to MTX, I'd say you're fine.
A forum community dedicated to Mazda MX-6 owners and enthusiasts. Come join the discussion about restorations, performance, upgrades, modifications, classifieds, troubleshooting, maintenance, and more!