Tuning Question

My friend is getting his turbo'd h22a civic re-tuned in a few months (AEM EMS). He's currently using an h23 transmission (the stock jdm h22a one blew a hole because of his diff) and is going to change to an Accord LX one (f22b2).

So here's my question, does it matter what transmission you use to get it tuned? Like if he uses the one in there now and get's it tuned, will it mess anything up when he changes over to an f22b2 tranny? I was just thinking that the different gear ratios may effect his performance from the tune. Like maybe the fuel map would be effected from making power at different rpms? Does that even make any sense at all?

nope, shouldnt affect anything, it may SEEM like it does because of the different gearing...but its not messing with anything.

Ok cool. I didn't think it'd make that big of a difference but I just wanted to make sure.

does not matter.