I use YNAB. I don't have any deductions for things like FSA, HSA, 401k, etc. I do have tax withholding as does (almost) everybody else.
I like my YNAB to be tax accurate. That is, for every paycheck, I enter the gross amount as income. Then, I enter as an outflow the taxes withheld for federal and state (I have separate categories for taxes).
If I had a pre tax transit flex account, here's what I would do:
Suppose a paycheck for $3000 gross, $100 in transit account contributions, and $300 in Federal withholding. I'd enter $3000 as income, $300 as an outflow in the taxes category, and a transfer of $100 to my on budget transit flex account.
Then in the transit flex account I would track the expenses incurred.