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ATSC does indeed use MPEG-2 standard transport streams. Keeping elemental streams in sync will be done by MPEG-2, and any residual time code streams left over from the production process are most likely superfluous.
Because OTA reception varies, what is recorded may not contain the whole MPEG-2 TS preserved intact, hence the need for products like VideoReDo TVSuite. But it acts on the MPEG-2 streams themselves. At this point there's no difference between MPEG-2 data coming from ATSC, QAM or other RF modulation schemes, as these have been out of the equation for a long time.
If you're having problems with MythTV, that's a completely different subject.
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