I gave up on the synced reading position at the same time I sold my Kindle, but I can live with that.
Getting stuff on the device is a bit of a hassle too, because I can't exactly go plug it in to my NAS, but exporting 50+ books to a directory and copying them manually takes a few minutes and I'm set for a year or more - so it's time well spent :D
Having everything (except for comics) consolidated in one place is the main reason I tolerate Calibre's quirks and eccentricities. It's ... opinionated, but it's still by far the best tool available for the price.
It will convert books to Kepub automatically and you can select to only sync certain shelfs.
Kobo can connect to Dropbox. They hide the option on older models but you can re-enable it with NickelMenu[1]. If you don’t want the Dropbox app installed on your machine, you can use Rclone[2] to sync files to it on demand. With a bit more setup, you can even set up Rclone on the Kobo itself and trigger it via NickelMenu to pull new books. This last part is a bit more involved.