Well, this is a bit of a grey area. If what you're asking (am a little slow on the uptake from your explanation heh) is wether someone who owns M2/Win and has the license to use Trojan with that, can create a patcher to use Trojan with AO M2/Mac then that stipulation lays with the portability allowed by the license in Trojan.
When you download and play Trojan you don't own it (obviously). You license it for a particular type of use (presumably this license is provided by the Trojan team). If that license specifies the ability to port the content to another medium (for example some software licenses allows a CD-R backup), in a usable and playable form, then yes, you would be able to port that content to something else. This is called emulation. The key with emulation is that you first, need to have the permission to emulate that content (the license) and that you need to make sure what's emulated is for all intents and purposes identical to the original form. You should not create a patcher or emulator for content you don't have the license to do so with. I think that's the stipulation you were wanting to have clarified.
The grey area lies in the fact of wether the license you get specifies the medium the content can be used in. If the Trojan team specifically does not say..."this is Trojan and should be used with M2/Win" or "Trojan shouldn't be used with AO Mac" then it becomes a bit of a guess, because their license doesn't specifically ban a medium, nor specify inclusivity. This is the same with music you purchase for example. If I buy a CD, I expect to be able listen to it if I put it on a blank tape, or if I put it on an iPod.
The other stipulation is wether this falls within fair use or not. Fair use is about what YOU do with content licensed to YOU, FOR you. If you have M2/Win, Trojan and AO and you want to create a patcher for yourself to ease your ability to play Trojan, that's probably going to fall withing fair use. However, you can't make said patcher available to others, or distribute the results of your patcher available to others. Individuals can re-invent the wheel each time to achieve said results.
I may not personally be very fond of the way things are like that, but that's my best interpretation. Again..I'm not a lawyer, this isn't legal advice etc etc.
Hope that also helps.
