No, unfortunately this is not controllable.
In earlier versions the problem was even worse (for players playing against Terran), because SCVs sometimes used to go completely inside a building, making them unclickable. Since catching an SCV at the right time (it being on the edges of the building) was sometimes completely up to luck, a lot of players complained about it (in particular in reference to SCVs building bunkers, where it was sometimes completely up to random numbers if you could defend against a Terran contain as Zerg or not), and it was subsequently patched in Patch 1.2.0
- SCV construction movement has been made more consistent.