There is a big difference between discarding units during the creation of the player's army, and doing so once the army is complete.
I totally agree with you that when building your army from a given list, you must do so under the constraints and assumptions for that list. Moreover, when providing transport upgrades for troops, there is a general (but occasionally unwritten) rule that transport upgrades must be provided for all units in the formation. So in your example of the Cadians, if the player elected to upgrade his Karskin infantry company with further infantry, he would have to buy 2x Stormlords (as the list intends). He might indeed also add three Sabre platforms for some AA capability.
However, once the list is complete I would allow the player to discard all but one of the vehicles so that the upgraded Karskin company could garrison. Doing so means that he has given up cost, capability and mobility for the potential advantage of starting on OW in an advanced position. If you had provided air-transport, I would allow him to discard all the vehicles (and some of the infantry) so that the formation could be air-assaulted into position on the grounds that he has then given up further cost, mobility and formation size for this advantage. Note, in a count-off, I would cost the formation at its original size, which would be 700 points in this case.
This is not a list design decision at all as the player is making these choices at the start of the game *after* he has built the army. Indeed, by not giving the player any separate WE transport formations (air or otherwise), you have already removed one of the the two occasions where the player might want to consider discarding units for some potential in-game advantage

As I see it, allowing a player to make these kind of in-game decisions is part of the richness of Epic. The potential advantages are matched by a number of costs, they are balanced if not slightly against the player taking these kind of gambles and they certainly do not detract from the game as a whole. However, I would suggest that this be an FAQ for the tournament scenario, not part of the 'core rules' as such.