MS provides updates to Office apps all the time, you can even subscribe to nightly and beta builds if you wish. You don't get that with App Store versions... you get the update when Apple lets you have them.
If there are issues with your purchase, MS is a LOT more helpful than Apple. Sad, but true.
Apple doesn't provide tech support with the apps they sell in the App Store. Getting support from MS with App Store versions is more difficult (not impossible). I'm not sure why, but it is what it is.
When you buy from MS, you get all the office apps, not just Word, PowerPoint, Excel and Outlook. You also get access to their other services, and you don't have to download/update apps like OneNote separately.
Finally, Apple NEVER puts things on sale. No coupons, no special offers, nothing—while MS often honors coupons and has special offers. This of course is only relevant at times of upgrades or the first purchase, but still... I'm not sure, but I don't know if Apple sells the perpetual (one-time purchase) versions of the apps in the App Store, while MS still does.
These were my findings when I first bought Office from the App Store years ago. It was just a royal pain in the behind. Last year I finally upgraded Office to the 365 subscription (which still allows me to install it for 5 users) and it has been so much better and quite frankly, just as easy.