Good question! And of course it is better, lets take an example:
Flat rate H.E.
You play with 0.75% H.E. and max win of 0.375% of Bankroll (1/2 kelly), for every bet with potential profit less than 0.375% BR, you use flat 0.75% H.E. Higher than that, you are not allowed to bet.
Variable H.E.
When you play with potential profit 0.375% of the bankroll, you still use 0.75% H.E. Lower than that the site will use lower H.E. instead of flat 0.75%. Higher than that, the site still allows you to bet with higher H.E. (remember that in flat rate, you are not allowed to do so).
That makes sense. But I'm guessing there is some sort of max profit cap? If your BR is
BTC23 am I allowed to place a bet with a potential profit of
BTC23 (with HE at ~40.5%)? If so, that's very risky for you.