How can I define which tone (eg D4) is to be used as a reference for the tuning?
This is part of the Scala .kbm (keyboard mapping) specification. If you put a .kbm file into the Scales directory with the same name as the .scl before the extension, Aalto (and the others) will load that mapping.
I'm working right now to release a revision to all the plugins that will fix some bugs in the mappings. So, if you think something is wrong, don't waste too much of your own time before deciding it may be my problem! And please post a report of what's going on.
Wow! Aalto understands .kbm - that's truely awesome. I'm not sure all synths that support .scl also support .kbm.
So big hands to you.
I think the documentation is behind on this, so sorry if it wasn't clear. I'll take a look.