IS Boxer does render all of the regions at the size of the largest region.
And then scales the smaller regions down to whatever size they are displayed at.

That gets you instant swaps between windows, no matter how strong/weak your system is.
Because they are already rendered at the larger size.
It also gets you extremely strong mouse broadcasting, for the same reason.

Depending on your system, that is definitely more strain on system resources...
Then a program like KC, which renders each window at the displayed size.

Still, it's not that drastic of a reduction.
If you're getting 50-60 FPS with KC, there is no way IS Boxer should drop you to 2 FPS ever.
50 FPS might drop to 40 FPS, or something similar.

Since Keyclone licenses are forever, it's pretty easy to test your system.
Give yourself a full playing session, but log in with the same number of accounts using KC.
See if you can make KC drop down to lower FPS in similar areas or after the same play time, etc.