Perhaps a dumb question, but I don't know what a "V.3 master spreadsheet" is. I don't know if that impacts my answer though.
The spreadsheet I use is based off the Your Money or Your Life book. I don't have any hotels or flights that are reimbursable, but I do have books, mileage, and food. Food gets counted as "work food" whether it's reimbursable or not (as a bill for entertaining a client and a bill for being too dumb to pack lunch both go in this category). Gas gets counted as "gas" whether I get mileage reimbursement or not (as its too difficult for me to count how much of the mileage reimbursement goes toward "gas" and how much is a prepayment on car maintenance). Same with books. Income goes as "reimbursement income."
It isn't perfect, as it inflates my expenses a little and inflates my income a little too. But this way I can clearly see what are "work expenses" that can be pulled out and what are "work income" that ties to it. Easy enough for my purposes.
Plus, by lumping my reimbursable expenses in with my regular expenses, I budget for my total expenses. The reimbursement check is then treated as a "bonus" to me and invested, rather than pre-earmarking it for a set expense. Again, works well for me but YMMV.