We are currently in the process when we would like to release a final version of Turris OS 4.0, but once we do it, there will be at least one more beta release as we want to fix a few issues, which was discovered by our beloved community and one of them is known - MariaDB.
Since Turris OS 4.0 is just a patchset for OpenWrt with extra feed (turris-os-packages). In the Turris OS packages, there are mostly our specific packages, which can not be sent to OpenWrt. You will find there some rare cases when we disagree due to different nature and want to take stuff in a different direction. As an example could be when we prefer user-friendliness and feature completeness oversize constraints. Others are in process to be upstreamed to OpenWrt/packages repository. We want to improve compatibility between Knot Resolver / Unbound and resolver-conf to rather implement something, which is compatible with upstream. Therefore, I shouldn’t forget to tell that we sent a lot of PRs to OpenWrt since January. Also, in Github pull requests to OpenWrt, we are helping our users, you can take a look here.
This means that what is in OpenWrt 18.06.04, that it is available in Turris OS 4.0. Same applies for OpenWrt 19.07 (Turris OS 5.0), master and so on. You can check file git-hash in repo.turris.cz in HBS/HBT/HBK/HBD/master folders. In that file, you can see which commits were used to build the release.
Before flashing OpenWrt, you may give it try with Turris OS 4.0 (with the stable release OpenWrt 18.06.04) and tell us, what you don’t like. Each feedback counts and we are looking forward to hearing that. Maybe in the future, you will realize that with OpenWrt, you are not supposed to use opkg upgrade and should look for new releases as from the time to time there are security vulnerabilities and you should be protected against them in time. In OpenWrt, you won’t be able to use all the internal storage, which is available as there is just 256 MB capacity for storage. It’s possible that they have changed since I tried it. In Turris OS releases, there is 8 GB storage available for you.
More details about the latest release of Turris OS 4.0, where you will find instructions how to give it try, if you want. If not, it’s your decision in the end. 
Let me try to help you with the issue, which you seems to be having. You are correct that sysupgrade is disabled in Turris OS, this one indicates that you are still having Turris OS. Since you have a UART cable, you can try to repeat steps 1. - 3. and see what it does in the serial console. I am thinking that the router was not able to find medkit, so it couldn’t proceed the reflash. Did you download omnia-medkit-openwrt-18.06.4-mvebu-cortexa9-turris-omnia-initramfs.tar.gz and put it to the USB flash drive and then proceed 4 LEDs?