Proto48 is just about track gauge and wheel standards, the rest is ego.
You can model to any detail level you wish no matter the gauge. You can model to any level of "prototype correctness" you wish no matter the gauge between the rails. There are very good prototype modelers in both Proto48 and Regular O Scale. It is more a matter of what you can live with.
I model in Proto48 and I am a rivet counter. There are others who are happy just putting the correct wheel sets in the wide trucks under R-T-R cars. It's all good, the only person that matters is yourself. If you are happy with your modeling at whatever level you choose, then just enjoy it. Don't worry about what someone says you have to do.
If you want cheaper track, then I think you should learn to hand lay your track. It's easy and goes much faster than you think. I would also mention to you that a 50 foot bundle of track goes faster than you think. Even when you build a railroad eight feet at a time.
To answer your question, I don't think flex track really matters in Proto48. Some love it, I'm hand laying most of my my rail. I want more rail size changes then is available in Flex. Your question never really entered my mind when I converted to Proto48.