There is some truth in what he has said, but he's a little behind the times.
Cannondale has adopted a lot of standards that are different than what the "rest" of the bike world has been using as commonplace.
Chief among those is probably the BB30 bottom bracket. ....thing is SRAM and FSA both have pretty stout BB30 crank options now. Not to mention you can get adapters to convert the BB to the other "standard" standard (can't remember the number) for threaded shell bb's.
The headsets also differ but srsly....who cares.
Buy what you want.
Ask the shop owner if you should buy any of the proprietary wheels that I am sure he has either on display or on half of the bikes he sells. Tell him the parts for those are only available through Mavic, Shimano or Campy and that they are expensive....see what he says....
Also...FWIW - Just about EVERY shop owner I have met in the last 20 years is grossly out of touch with what the latest in the industry is. They usually barely know what their reps have been telling them. That's because they are busy running their business and moving hybrids out the door.