In my opinion you are OK the .003 inch wobble is likely well within their specs for the engine. The non-prop driving side of the engine doesn't get the attention that the other prop-driving side of the engine gets.

The utility engine designs tend to allow for quite a variation in tolerances so the .003 inch thus that wobble may be perfectly fine for it. A more precise engine design may have more tight tolerances, but even then the .003 may be OK too. I would test run the engine and see how it does. One problem is the gasoline engines tend to all vibrate more anyway so that .003 wobble may be fine in anycase.  Oh yeah, made using "less exacting tolerances" is the phrase they tend to say about them. Plus if it is not the propeller shaft side of the engine, then they usually don't care much, if any, about additional wobble there. The propeller shaft side of the engine with the flywheel and magneto needs more tight or exacting tolerances as a tiny wobble there can really magnify the vibrations and reduce power more.

Many of the low end trimmer engines, etc., use a pressed steel and or stamped steel crankshaft and can be pretty liberal on their tolerances for what is Ok and not Ok as to measurements.

Now then the better made for RC high performance gasoline engines are made to much more exacting tolerances as that yields more performance, etc.  But most of them went with cantilever crankshafts supported on only one side and dropped having a full length crankshaft.