I wonder how Mike came up with this loop placement. Considering him a great amp builder, this is probably the worst loop ever designed, if it's an afterthought as you say, I get even more puzzled.
Beside of that. If you are not using the loop and it is there, it will not make a lot of difference. If you plug something in it, it will suck tone like a madman, but that's only my 2 cents, like my statement on fixing the loop results in change in tone.
IMHO the SLO circuit has it's flaws but it sounds unbelievable as it is. Any SLO I heard "fixed" next to a stock SLO sounded inferior. To me.
I guess "majik" is that pretty fragile balance of flaws and goods and their interaction dancing in the verge of instability in that circuit.