I have a similar unit, but mine has a tank, with a 3 gallon capacity. It works fine, too.

I think you may be on to something, though - pressurize it to 90psi with the compressor and hit it a few final licks on the manual pump to get to 100 psi.

Now, I dont go too much by absolute pressures and rarely actually measure the fill... I go by feel and I take it slow. The reasons why are explained above.
But, I'm guessing you are following manufacturers recommendations for the tire and/or bike, and want to be precise?

PS - What I do is just "air it up," a little at a time, until the tires are really hard or haven't popped/herniated, etc. Then I test 'em on the road. If it feels like it aint right, I air it up some more. Repeat as necessary. I'll use a tire guage if I have any doubts... and if I can find one around the shop.
(It aint scientific I know, but thass' kinda how we do things in my part of the South )