You can certainly negotiate a long term service contract prior to installation, but what if the company doesn't live up to their promises? what if the response time and and communication from the OEM is terrible? When your married to an OEM's equipment it doesn't leave much recourse. Now I will say most of the big guys do have competitor engineering departments that develop tools and manuals to work on competitors equipment, but that still does limit a owner to a hand full of companies other than the OEM for service and if it is newer equipment it could be years before anyone develops 3rd party support.

The controller modification can be an issue but its been my experience that the cost of the non proprietary modifications is no where close to the cost from an OEM. If you need software almost all the major OEMs will require one of their mechanics come out to load the software which they of course will charge a good amount for. You won't have that issue with MCE,Smartrise,Virginia controls,GAL ,etc.

Also lets not forget the proprietary mechanical items like belts, machines and special sheaves. The OEMs might sell them but at 10 times the cost of standard parts.