I get it now. I wish I had some insight for you but this is unchartered waters for me. The things that spring to mind immediately are how involved are you going to be in day to day operations, what type of work (service, construction, resi, comm, large small), how big is the shop, what type of backlog are they looking at, what kind of experience does the staff have, if you agree to flat rate and they don't make it how will they honor the agreement, how long is the contract,will there be provisions for renegotiations at some point in the future and so on.
I have no legal insight into this but for me it would really come down to what I thought this business was capable of. It would be a sure bet and less headache to take the flat rate. It could be a roller coaster ride and certainly more paperwork and negotiation to take a percentage. You would have to verify the work and would you get paid what they bill or what comes in the door. If they bill $10,000 to a customer and get stiffed do you get your cut of that regardless if they ever see the money?