Having had "Motorola Built" systems under my control before, it's hard to say. A lot of it depends on who is actually doing the work.
Some guys will make sure it's all done right and do a great job. Others will cut corners every chance they get. Just because it's "Motorola" doesn't mean anything about the techs.
The issue is when Motorola comes in and does one of these jobs, they do -everything-. Ideally you want an outside consultant or local Subject Matter Expert (SME) that is separate from the project that can watch over things. Making sure the job is done to spec, done to code, and done right is important. Relying on the company that sold you the system to do that isn't always a good idea.
As for specific things to watch out for…
Specifically with Motorola, make sure they do not enable ANY AND I MEAN ANY! proprietary features on their system that will lock out any other brands of radio. Used to be that Motorola was really good at enabling the "free" ADP encryption on their radios and that would lock out all other manufacturers. You would basically be stuck buying Motorola radios for the rest of the system life.
Do NOT let them do this on your system.
Also, make sure that they do not read, write, or read/write disable ANY of your radios. Some shops will do this in an effort to make you go through their specific shop for any changes, reprogramming, etc. Remember, they are YOUR radios, not Motorola's, not the shops, etc. You need to have complete control over your radio system. That means no one is allowed to force you into using a specific shop for all your equipment and programming for the life of your system.