In simple aircraft like fixed gear singles, the owner will do maintenance on tacho time - most tachs in these are set to match watch at 2300rpm, and because the owner is doing his /her maintenance on this system, then thats what the a/c hire in/out rate should be based on (fuel burn is also directly proportional to RPM).
Most of these simple a/c on crosshire are also fitted with a VDO running off either oil press or master, for the purposes of easily recording the time an instructor is sitting in the RHS. In either event, during circs VDO will be about 10-20% ahead of tach, and on a crosscountry at 75% power VDO and tach will be the same.
For reasons stated before, training/endorsements at reputable outfits will be on VDO, and PVT hire on tach.
The charge in method is negotiated with the owner (at least with X/hired a/c) at the time of putting the machine on line.
More complicated aircraft are another story - generally the way the owner does maintenance should be the way the a/c is hired in/out - instructor time always being master on to master off.