I didn't realise per-table timestamp precision was a thing because it is missing from the python API, but is present in the RPC API:
https://cloud.google.com/bigtable/docs/reference/admin/rpc/google.bigtable.admin.v2#google.bigtable.admin.v2.Table.TimestampGranularity

It's REALLY not obvious that the table is in ms precision by default, and is silently dropping usec (granularity isn't mentioned at all in docs I've read). This wasn't visible to me until I happened to try and filter by a value that didn't divide evenly into ms and got:

Timestamp granularity mismatch. Expected a multiple of 1000 (millisecond granularity), but got 500.

This also explains some of my problems in:
#2397

although the InvalidChunk problem might be independent.