Bad plans are just part of the trade, and anyone doing commercial work has seen their fair share. The idea here is to sell the job and make money, so figure the job as shown, then propose it as a base price with any adds you know they will need, and with a very specific scope of what they get for that price. My standard scope letters have 63 points what is furnished and what is not. Thinks like I will furnish temporary lights and receptacles but consumption is covered by the GC. Who furnished the dumpster? How about the painted plywood backer boards for the telephone? Who does the control wiring. It’s easy to miss the small things with bad plans because its just not shown but it will be expected.
If a fixture they specified is no longer available, then put an allowance in for it, and say in the proposal that they light fixtures specified are not available but you are carrying $X for a allowance. The GC will appreciate you putting something in for it, and when you do submit an alternated they cant go over your allowance without giving you a change order.
You need to be very specific, on what they get for your price, and be VERY careful they don’t sneak anything you don’t have covered back into your contract, should they decide to use you.