We had a similar runway incursion a while back with a vehicle that had been given clearance to operate 'all areas' to carry out a lighting inspection. The procedure for the inspection is to check all the runway lighting, including lead on/offs followed by taxiways North then South. The driver checked the runway lighting and vacated north side, 10 minutes later crossed a runway holding point to continue south side. The ATCO had removed the blocker strip from the runway bay and on seeing the vehicle cross at the stop end filed a runway incursion (no aircraft involved luckily).
Personally, if I have given a clearance for a vehicle to operate on a runway or 'all areas' I would want either a runway vacated call or an acknowledgement of an instruction to remain north/south/east/west of the runway before issuing any take off/landing clearances. Where I work it's common for a vehicle engaged in wildlife scaring to drive towards/over holding points to encourage the wildlife to leave the runway area before turning back onto the runway to continue the inspection/wildlife removal operations.
For aircraft/vehicles crossing, providing that they are in sight of the ATCO and workload is such that attention is not likely to be diverted elsewhere, I don't see why a vacated call is going to make operations any safer and is just unnecessary RT imo.