How to correctly compression test with electronic throttle?

[terdcivic]

because each cylinder would be affected the same

This is true if you're just trying to make a general assessment of a street car as "not busted".

I suppose if you're trying to get a more accurate picture you'd be doing a leakdown test instead.

Yea, a leakdown test is much more accurate. Comp tests are only for seeing if it isn't broken. Leakdown tells you exactly what % each cylinder is leaking at tdc (with all valves closed).