Your first paragraph is my entire point: you are theory crafting.

every flamer he is paying just about the cost of a base of scarabs at 5+7pts.

Infantry squads are 4 pts/model, not 5. Were you aware of this?

In either event, regardless of how may scarabs you have, each charge against a squad with a single flamer means eating up Overwatch. Per 8th ed rules a squad can overwatch every time they are charged, so long as an enemy model is not within 1".

one will do 2 wounds on average

The mean of a random d6 variable is 3.5; not 2. I can understand why it would suit your viewpoint better to assume 2 (given that scarabs have 3 wounds per base) but your estimated value is mathematically inaccurate.