Well Rioven,
The only solution rooting (hacking) is the one available at the moment. Erel is right, if you really have a need to be sure you can run this on the Atrix, you are probably best off spending the $25 bucks so that you can upload it to the Android Market then install it onto your own device from the Market (that's how I would do it in this case).
The other alternative is wait until someone has a well tested SBF file (basically a copy of the stock ROM for the Atrix) then if you wanted to root instead of always having to rely on the market simply to test your software, you could root it, do your development, make sure it works as you desire, then restore it to stock via the SBF.
I can't for the life of me figure why Motorola would have taken this stance with the Atrix. I can speculate, the least of which not being how it may have operated with their webtop solution and the webtop dock. But even at that, I just dont get it...It's almost the antithesis of Android in the first place.