Yeah, can't deny that the account linking procedure is quite frankly, sloppy to say the least. When Destiny 2 moved from BattleNet to Steam, all anyone had to do to move, was to go to their website, and login with bnet and Steam, it was done in 2 seconds. This website already lets you log in with both, they have the base login procedure done here already I'm not sure why they didn't just put it in the website like most games would do.
As for Windows Update, windows update and the windows store all the use same backend software for file delivery, so if anyone happens to try to modify windows update to try to hamfist it not to update something they don't want updated or some such, it's very likely going to do things such as break things like the windows store for example.
It's pretty cheesy they did this this way too, since a huge patch arrived at Steam launch as well, meant everyone that was hanging onto the windows store version, planning to move, still had to install that huge patch before they could move. Glad I'm over on Steam now though, should be more stable than the windows store I hope, had that darn thing uninstall my game like 4 times.