At a design level, the biggest difference is in design for intensity of utilization. That is, operating cycles per year. An RJ designed as an airliner is intended to operate on average, about 2500 cycles per year. A corporate jet typically operates under 500 cycles per year (although with a charter operator or fractional ownership operator or a corporate shuttle they may run 1000 cycles plus).
The utilization drives the level of robustness required in structural and system design. A purpose built corporate jet put into airline use would have much lower dispatch reliability because it's getting beaten to death (like putting a luxurious but fairly lightly built car into service as a taxi). At the opposite end, you have regional airliners that are sold as business aircraft. These airplanes are overbuilt for their role as corporate airplanes and have a reputation for being pretty bulletproof.
Production wise, the biggest difference is that corporate airplanes are built at a lower rate and are almost always delivered "green" to a completion center selected by the customer to get the interior done (by Supplemental Type Certificate), whereas regional jets get their bus interiors done in-house. There are a few exceptions to this (some Global Express interiors are done in-house by the OEM). And the interiors themselves are built to a completely insane quality standard - I mean, the interiors have to be absolutely perfect when someone has 5-10 million just into the interior.
On customer acceptance on a corporate jet, the customer's acceptance team will be going around the interior while the airplane cruises at altitude making sure all the panel gaps are still straight with the hull pressurized, in addition to making sure everything related to the interior works (like plumbing doesn't freeze etc). The slightest flaw requires rework. God help you if you ding the woodwork...