Actually, I believe they are. The ECU has tables for both auto and manual. At least the stock ECU, and the T5Suite Stage I-III. I know that's the case for 9000s, possibly there is something different with the NG900s, but the bin file I pulled down from ecuproject for a NG900 contains both boost tables.
I think it was up to the tuners whether they tuned both maps. If you told them the car was a manual, they might only modify the manual maps. Of course, they may just have a preprogrammed map they dump to the box. I noticed the T5Suite changes the maps for both the auto and manual. The auto maps have a lower boost request, but more than stock.
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