On an auto trans - the same way as you are supposed to on a manual trans bellhousing. A little harder to get in there but take your empty trans case and bolt it to the engine.

Take a magnetic dial indicator assembly and attach it to the cramkshaft.

The indicator proble should touch the OD of the pump bore - that checks bore runout.
The indicator probe should then touch the gasket face of the pump bore - that's face runout.

Spin the crank to get TIR ( total indicator runout ).

Look in a service manual for the procedure - and I think it was also called out in the old Direct Connection manuals.

As long as you have two good dowels in the engine and the trans case bores for those dowels are round and not egg-shaped you are normally good. I can't recall ever having a need to install offset dowels like we did on manual transmissions. The flexplate is more forgiving than the flywheel. Plus the converter internals are forgiving too.

When you add pump bushing to converter clearances, internal converter clearances and the flexplate flexibility that provides more flexibility than the manual trans stack up.