I understand every locality is different but I am wondering what the timeframe of your experience was, how easy/difficult it was to get the modular/prefab building approved, whether it was classified as a building or something different since it was modular as well as the square footage of the warehouse you constructed. 

I imagine that the cost of lumber has skyrocketed since your project, and can thus seriously impact the total cost.Why did you choose the particular square footage that you did?

@Caitlin Worrell  Is it possible that the additional bedroom and square footage was never permitted, and the tax records show the lower bathroom count and square footage? 

For example if you occupy 50% the house (based on sq footage, #of bedrooms)than you can allocate 50% of the capital gains at the time of sale towards the section 121 exclusion - the remaining 50% will be treated as investment income and possibly subject to depreciation recapture -this is assuming you are apportioning your mortgage interest and property taxes on the proper schedules when you file your taxes ( your CPA should be able to help you with this)I would love to have CPA weigh in and maybe they can provide some insight as to why you might be getting that advice

An appraiser would look at your house, compare square footage, location, amenities, number of bathrooms and bedrooms, etc. and come up with an ultimate value. 

Sometimes if the job is under a certain square footage and not structurally invasive you just need someone to draw up what youre doing for the permit.I do know that across the board, you usually do not need specific plumbing, elec, drawings for permit.

We did a $60k remodel and when we refinanced it 1 year later he only increased the value by a small amount because the square footage didn't change.

Multiply your square footage by comp square foot and that would give you a decent idea. 

Square footage could have a huge cost variance or no cost variance.

Created master bath and master closet space within the same amount of sq footage.