This may not be currently possible. The ~a expands to full albums, but adds tracks based on their FileKey instead of Disc#/Track#. The Filekey is assigned on Import and, depending on the order of the files on the actual filesystem, often doesn't match the disc/track ordering.
Some possible fixes on MC side, ordered by complexity:
1. change the ~a modifier to preserve disc/track ordering
2. change the ~a modifier to preserve and copy the existing seq number to all added tracks, instead of resetting it to zero as it does now - ie, all tracks for first album would get seq=1, tracks of second album get seq=2, and so on.
This would allow:
~seq ~a ~sort=[Sequence],[Disc #],[Track #]
3. add a new Sort mode or modifier like [AlbumSeq] to sort tracks within albums, while still preserving the current album order
4. add an optional field list to ~seq, like ~seq=[field1],[field2],... . The would assign Seq numbers that increase only when the mentioned fields changed. With this you could write:
~a ~seq=[Album Artist (auto)],[Album],[Disc #] ~sort=[Sequence],[Track #]
The ~seq here would also assign the same Seq number to all tracks on the same album, and then the ~Sort would use that to sort the tracks while preserving the general album order.
