Not really? Let's say Tom gets the BiS item Inscrutable Quantum Device from a +6 (so ilv 200) but Tom only has KSC (+10s in time but working on KSM). Sure he can upgrade to 210 (2 levels at 400 valor each time). So he's down 800 valor (out of 5000 via seasonal cap). Let's say in 3 weeks he finally gets KSM done by then the seasonal cap is 7250. Assuming he's done enough callings and M+, he can then upgrade that same IQD from 210 to 220 (another 3 levels for 1200 valor points total).
The only thing that might screw over Tom is if he also gets a IQD from the GV at higher than ilv 220 but what are the odds? Even with 3 choices unlocked the dungeon pool is vast.