I went to refinance the property into my name and realized I hadn't budgeted the closing costs in.

In our budgeting, we are absolutely (now more than ever) counting on receiving the stated commission.

Who budgets their rehab perfectly? 

Typically as a PM you will oversee employees, handle budgets, help set leasing targets, etc. and this is all relevant info as you start underwriting your own deals, seeking financing and talking with investors to raise capital.

Have you seen their budgets, do governments make money (not litterally)?

Amazon delivery, truck drivers, Uber Drivers, Certified Nurse Assistants, School Teachers, City Workers.It looks like the government is cutting checks to our tenants.

Even if the project lasts 3 months, that is "only" $1200-1500 dollars, which on my rehabs is almost meaningless and only a small part of my overages budget. 

All costs you need to pay out of pocket that is not in the rehab budget. 

Perhaps its worth both bumping up capex and budgeting for future improvements.

I haven't forced them to use Cozy but provided them the option with the benefits of:-accepts split payments for easy in budgeting-builds credit for future car or home purchases-no driving to the post office or paying for stamps-electronic receipts-can setup Auto transfer so you don't need to worry about it-no fee-accepts credit card payments for challenging times (like now)