Number of bytes increases while removing lines of code - Too big to save to flash

Yes, I'm not sure. I think at some point we did suggest that you use minification to get the code size down, and that could have been it?

It's fixed now, so when I next update the Web IDE you should see the improvements.

why isn't the remainder more in line with a common 2n multiple?

That's an easy one. The chip itself may well have 32/64/128/etc bytes of RAM, but other things use that RAM as well (execution stack, wifi, etc). Espruino uses up what's left, which is pretty much guaranteed not to be a nice round number.