You can check runout off the machine - it may be that your 'wobble' is coming from any or all of a number of places: the bearings in the spindle, a cheap collet or a less-than-straight bit. Wobble isn't really an artefact of the router gantry, unless the gantry is loose or the spindle mount is loose.
If the spindle isn't straight in its mount, or if the gantry isn't square, there won't necessarily be any wobble, but the cut won't be 100% perpendicular. My first build didn't exhibit unacceptable runout at the tip of the bit, but it was clear that the cut wasn't 100% perpendicular - easy enough to check, just plunge some holes using a small bit and the hole, viewed from above, will be slightly oval.
With runout, the hole will be larger than the bit, as the runout will be likely to be equal throughout 360deg. Easily checked by pushing the bit through the hole by hand - it should be a friction fit.
If the runout is more to one side, that's more indicative of a problem with accuracy of the mount.
Does that make sense?
You don't mention what spindle you are using.
I've used a few, from a cheap Chinese air-cooled to a more expensive Chinese water-cooled with Japanese bearings to a German air-cooled. They all exhibit 'some' runout, but the water-cooled and German spindles were negligible for my application, which was cutting ply and mdf - I got more tear-out from the bit than I got inaccuracy from the runout.
I make audio devices and have been contracting out the cutting of my faceplates (by laser), but with more practice cutting alloy (to get the rate and feed right), I would be confident that my German spindle, with the right bit, would give me an acceptable result.
But, I would be wary of cutting precision-fit components down to small fractions of a mm. Within half a mm is well within spec of what I need.
If your runout is less than the accuracy you need, it's acceptable.