To answer Honestone....I always update directly from the app store app when Apple tells me to.
Yes, I also get the original Mac OS from the App Store. But for updates, in most instances, I'll download the Combo Update, and I get that from Apple's site. I am not even sure if it appears in the App Store.
Now, my question was not about where you obtain the update. It was more about the update process itself. I actually did not get the initial version of High Sierra, as 1) there were too many serious issues with that release (especially with this new APFS stuff), and 2) not all of my third party (non-Apple) software was compatible with High Sierra. There were some updates for such compatibility for some of the programs (most were actually OK), but not for three critical ones: Tech Tool Pro, Onyx, and SuperDuper!. The same was true when Apple issued the first update, OS 10.13.1. Yes, a number of bugs that were in V10.13 were eliminated, but Micromat was still working on a version of Tech Tool Pro. Finally, in late November, Micromat released an update for Tech Tool Pro. Shortly thereafter, Apple released V10.13.2. I downloaded that full OS from the App Store, then via my SuperDuper! backup, erased and formatted both of SSDs inside my Macs, did a clean, fresh, "virgin" installation fo OD 10.13.2, and finally via Migration Assistant, "migrated"/copied all my needed "stuff" from the SuperDuper! backup.
For OS 10.13.3, I upgraded by downloading the OS 10.13.3 Combo Update and applied it.
There are a number of folks who download an update for the new Mac OS, and just apply it to their current system. For example, if one is running the last version of Sierra, OS 10.12.6, and then decides to "move" to High Sierra, one way is, yes, get the update from the App store (whether Apple prompts you or not), and have it just update Sierra to High Sierra. But there are times that method can cause issues, especially if one has done very little (or no) disk cleanup/maintenance/repairs (of course a backup is mandatory). Then there is the issue of third-party compatibility with the new OS.
No matter how one "upgrades" to a new Mac OS (or even just to update the version within that OS), it is just about mandatory to get prepared for such an upgrade/update. Not doing that can result in issues, some serious, some not so serious. My attitude is "Better to be safe that sorry".