You know this has never been mentioned to me before and I send files all the time to SWX and others. I haven't experienced and repercussions for it.
However, if this is the case then I would simply continue to model as I always do and when I'm ready to send files, rotate all the files to the correct axis. orientation.
To be honest, not sure why SWS and IV chose the Y axis for up, Z makes more sense. I can only assume its because they rely heavily on sketching, just a guess.
Hope this helps