IMO, faster updating is a minor benefit to this since, as @Logoffon mentioned, it can just be done overnight or even just when you don't need to use it for several minutes. The safety aspect of having protection against a bad update bricking the phone is much more important and worth sacrificing a little bit of space, especially if, as the author noted, and I was thinking as I read the article right before they mentioned it, the OEMs just include an SD slot, something I consider essential anyways. This is just another example of many of Samsung not following standards and doing things their own way, which sometimes leads to an improved experience but quite often leads to a worse one, and is one reason I'm unlikely to buy any more Samsung products.

As for OEMs using A/B to prevent users from flashing custom firmware, I suppose anything's possible, but that scenario seems rather unlikely, both due to the technical challenges of implementing it and because if they wanted to prevent flashing a custom ROM, they would just lock the bootloader, which for most who want to use a custom ROM is reason to avoid a device/manufacturer. And if they don't lock the bootloader, it wouldn't make much sense to use the A/B system to prevent custom flashing, and if they did it would result in massive backlash.

Storage consumption aside, it would still wait for the user to reboot their phones anyway, just shorter downtime, when they can just schedule the update installation during the their bedtime or inactivity.
Not to mention that this could also give manufacturers ability to strictly forbade installation of custom firmwares by having the partition automatically restored whenever the system partition is modified by the user.