Been away for a bit and misses quite a number of posts but yes you're correct in your wondering
The TC is pushed fully into the transmission so presses hard against the pump. Then when the transmission is bolted to the engine there should be a 1/8” gap between the TC and Flex plate. As such you then pull the TC away from the transmission pump by that 3mm gap and bolt it to the flex plate. Doing that will ensure the correct clearance between the various parts so that any growth in size (ballooning) of the TC as it gets hot won’t cause anything to bind up (thus avoiding pump damage or trust bearing damage).
Who‘d have thought a TC could balloon 3mm during operation
In older transmissions, as I‘ve understood it, production tolerances were much worse that those of today. As a result of old school‘s poorer production tolerances, fitting a transmission required lots of checking. Mechanics would usea straight edge and measuring TC bolt boss to bell-housing bolt face distance (1) then measuring the engine block to flex plate bolt face distance (2). With a little maths, one could work out the TC to flex plate clearance (3=1-2) and ideally that would be 1/8”… If the clearance (3) was much larger, spacers and appropriate length bolts would be used between the TC and flex plate to ensure that important 1/8 clearance existed. If the clearance wasn’t sufficient, they’d machine the bosses an appropriate amount to ensure the correct clearance. Such issues around machining or spacer use simple aren’t an issue these days with high tolerance high dimensional quality manufacture
Much of this was mentioned in the video I posted (and/or the video I couldn’t find and link to)
Skid factory YouTube change also goes into a lot of this TC clearance stuff and the reason for its importance (TC ballooning during operation causing crank trust bearing failure or pump failure is no clearance)