TT, I shoot for around .020" max. and I'm real happy if I get .010".
That's with a QUALITY alloy rim like excel, DID, Akront etc. You won't get that with chinese rims. And often the weld seam won't fit into those tolerances. So I kind of discount the seam...you might not see it by eye...but you'll find the seam no problem with the indicator.
I pay a tad more attention to getting the axial runout good...the bike will tolerate more lateral runout than axial, you'll feel the axial more.
But even .030-.040" is usable without a problem if the rim just doesn't want to straighten out....depending on what tire you use it's rare for the tire itself to have run out less than that.
Also depends on how fast the bike is...a runout or balance that's acceptable at 80-85mph might not be at 110 mph.