how much
removing the intercooler would affect partial throttle operation.

a quick guess would be that you might be courting overheating issues.

The engine pushed full displacement air through the engine idle or WFO, with
the slight difference that when the engine is very lightly loaded the turbo
pumps out less extra air. My guess is the engineers have "tricked out" the
turbo to give more or less full umph from maybe about 1/3 throttle on (just a
guess, but some figure less than 100% is a for sure).

Taking out the (designed in) intercooler would force less dense and hotter air
into the cylinder.

Is that a problem? I'd guess you would want to talk to a design engineer on
that one. You have both the issue of less dense/hotter air and the issue of
what's the right fuel amount for that air.

I dunno. I think I would be inclined to call the factory and try to skip
around inside the company until you can find an engineer type who knows his
business and doesn't normally talk to end users and is dying to help someone
out.