Almost all manufacturers’ stock shafts have limited variability in length and shaft flex/frequency. A driver that may be listed by the manufacturer as 45.5” may in fact be 45.25” or somewhere slightly in between. I was formerly on Ping’s staff program and received two Ping i15 hybrids with stock TFC stiff flex shafts. Inconsistencies in performance prompted me to check the shaft frequencies of each. The frequencies of each shaft tested as a regular flex (soft reg. at that). However, I did not have similar issues with the stock driver or 3-wood shafts. Each tested well within the range for a stiff flex shaft.
Your best bet will most often be going through custom to request that your shafts be frequency matched or to go with a custom/exotic shaft if you still have lingering concerns with the quality of the stock shaft. This will add significant wait time before you’re able to hit the links with your new club, but may be worth it.
Alternatively, as you know some facilities and stores are better equipped than others. You can ask the Pro at your local store or Pro Shop if they have a shaft frequency measuring device. If buying off the shelf ask them to test a couple of the same club to see which one best matches your needs. The variability may surprise you.