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.
Late reply, but
93 MX6 V6 KL01 can use but your rad fans will run constantly due to a missing sensor on 94+
94 PGTv6 KL55
93 PGT v6 KL07 can use but your rad fans will run constantly due to a missing sensor on 94+
There is a post somewhere that lists all the ECU models and the year make and transmission type
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