I use YNAB and do take home pay. The way I see it, the other expenses don't need management. I know I'm maxing out my 401K, I can't control the cost of health insurance. I do handle tax planning, but that is outside of my budget, which is mostly for daily planning, short term savings goals, etc.
The only downside I can see is that when I look at my annual spend, I'm missing things that I would eventually (in FIRE) have to manage, like health insurance. Also, this is small, but I put spend on health FSA items in a holding account, and then when I get reimbursed, the reimbursement wipes out the expense. But these are not huge amounts. I would just have to adjust for them when I look at FIRE numbers.