Emergency exit and seating design is controlled by the aircraft certification process, not through the operating certificate. Operators may not exceed the certified seating capacity. Part 25 covers larger commercial aircraft including the BBJ and similar. Part 23 covers general aviation. Here are excerpts:
Part 25
14CFR25.807g Type and number required. The maximum number of passenger seats permitted depends on the type and number of exits installed in each side of the fuselage. Except as further restricted in paragraphs (g)(1) through (g)(9) of this section, the maximum number of passenger seats permitted for each exit of a specific type installed in each side of the fuselage is as follows: Type A 110, Type B 75, Type C 55, Type I 45, Type II 40, Type III 35, Type IV 9.
Exit type in Part 25 is specified by door size and location.
Part 23
§ 23.2315 Means of egress and emergency exits.
(a) With the cabin configured for takeoff or landing, the airplane is designed to:
(1) Facilitate rapid and safe evacuation of the airplane in conditions likely to occur following an emergency landing, excluding ditching for level 1, level 2, and single-engine level 3 airplanes.
(2) Have means of egress (openings, exits, or emergency exits), that can be readily located and opened from the inside and outside. The means of opening must be simple and obvious and marked inside and outside the airplane.
(3) Have easy access to emergency exits when present.
(b) Airplanes approved for aerobatics must have a means to egress the airplane in flight.
Part 23 was rewritten to be objective oriented rather than regulated by specific design. The means of compliance now contains all the specifications that used to be in the regulation. The original regulation may be used in many cases but alternate means of compliance can also be proposed and used if approved. Getting approval for a means of compliance is not trivial, so it can be easier just to use the original reg.