What's "a few years"? If the fit-out will not happen for several years, there's a good chance a new code will have been adopted, and the fit-out will have to comply with all requirements of the new code. The building won't have a certificate of occupancy, so it won't be allowed to be used for any purpose. In fact, it's possible that even storing materials and equipment for the future fit-out may not be allowed.
Further, if (as should be expected) the energy code becomes more restricted, any mechanical equipment purchased now may not comply with whatever requirements may be in force at the time you (or your client) seek a permit for the fit-out.
We recently went through that with a business in town. The owner took out a permit to erect a pre-engineered metal building, to be used as a warehouse and offices. He applied for a shell-only permit. We tried to tell him he'd be better off doing it all at once, but he insisted. His design professional assured him there wouldn't be any problem.
There were problems. The state adopted a newer edition of the ICC codes between the time of the shell permit and the application for the office fit-out permit. The design professional couldn't (or wouldn't) deal with the code changes. Ultimately, the owner fired that design professional and brought in someone more competent.
In your case, apparently your client doesn't have the money to do the fit-out at this time. That's a fact. But IMHO it's a mistake. As to submitting both sets of construction documents at the same time -- why? If you get a permit for the fit-out now and then don't pursue it -- the permit will become void in 180 days, so what's the point?