There are some interesting points here. I think there are two possibilities for the way the uprights were planted:

1. They were raised and backfilled before the lintels were fitted, this would require on-site cutting of the mortices since the positioning of the uprights is not likely to have been accurate enough.

2. They were raised, but not completely backfilled so as to allow a degree of adjustment to match the tenons to the pre-cut mortices.

It's interesting that some of the lintels have two sets of holes. Perhaps these lintels were pre-cut, but then had to be re-cut on site. Is it possible that they began using pre-cut holes, but then changed to on-site cutting once they realised how difficult it was to achieve good alignment?

If the uprights were securely planted and had good flat top surfaces, the weight of the lintel should have been enough to secure it, so perhaps the joints were designed more to keep the uprights in place. Or, since the tenons are conical in shape, perhaps they were a construction aid to help guide the lintels into the correct position.