I know the new Game Shape hit is meant to deter large purchases prior to cup games, but this will affect club, and particularly NT teams, as well. High salary players tend to sell more often, and having consistent game shape decreases affects not only NT planning but also training (if an NT player is transferred, they will need to waste a week to train Game Shape just to stay relevant). Coaches cannot guarantee any player will or won't be training, getting proper minutes, or for sale, at any given time and this just adds another factor out of their control that may seriously affect the outcome of NT games.
I think the idea to limit the advantage of buying players at the last minute for Cup games is on the right track, but if you're causing game shape decreases, be aware it affects multiple areas. The GS hit must be small.
I think your points are something that would need consideration, but I think that if the changes are considered to be good for the core game experience (clearly, the BBs think so, otherwise this wouldn't be in place) then any inconvenience to the NT structure shouldn't be an impediment. One could hope that this might finally be the last nudge needed to get people to stop training players that are unaffordable and only exist to play on NTs, but I'm not sure I've got that much optimism. ;)