Of course that spacer changes things. But who cares? You have to check that the rim is centered anyway. Just don't wait until the spokes are fully tight. Do it half way. (Yes, you can do it with the tight spokes but that is living life the hard way. And, sorry, no one is going to award you points for extra effort or rounded nipples.)

Oh, if you don't have a dishing tol and the stand doesn't provide a solid, repeatable location for the axle, use your bike as a dishing tool. Put the wheel in and slide it to hard against the end of the dropout or track end slot and tighten the nuts. Measure rim to chainstay on the left side. Now take the wheel out, flip it and put it in the same way. Measure again to the left chainstay. Should be identical. If not, just tighten one side as needed until it passes the test.

Don't sweat what you have to do to get chainlines, spacing, etc. Do what's needed, preferably before the wheel build. Then build a centered wheel. That simple.