Jobst Brandt's definitive text "The Bicycle Wheel" has this to say on spoke tensioning:
With tensioned wires as spokes, the wheel can support loads only to the point where its spokes become loose. At this point the wheel will collapse. Therefore, for greatest strength, spokes must be as tight as the rim permits. Structurally the
rim supports spoke tension as an arch that is compressed by the inward force of the spokes. The load limit for most rims is far less than what the spokes could deliver if they were tightened to their breaking point. So in a conventional wheel, it is the rim that limits wheel strength, not the spokes. A rim can be subjected to spoke tension near its elastic limit because, during use, almost no net tension increase occurs.
In practice, however, spokes should be slightly looser than the maximum the rim can sustain, because at maximum tension, failure of a single spoke can severely deform the rim.
Given that strategy you should not tension the wheel based on any additional compression from the tire and tube, since getting a flat could result in rim deformation or damage.
"The Bicycle Wheel" provides the equation for the decrease in spoke tension under tire constriction, if you're curious. His measurements on a 36-spoke wheel with spokes at roughly 100kgf and a 25mm tire with 45-degree cord at 115psi give a reduction of total wheel compression from about 5700N to about 5300N.
In practice you should verify that your spokes decreased in tension evenly; if they didn't you should ensure that you properly stress relieve the spokes and retension them.