Yes, the calibre error is a sign that the database on the Touch is corrupt and needs to be rebuilt. I suspect that the bookmark problems are because of this error. The only real fix for this is to do a factory reset then let the Kobo desktop app update it to the latest firmware.
As to newer calibre versions and the Touch, they are fine. Apart from the thread you refer to, there are plenty of posts here about this. Just follow the instructions in the warning message that calibre displays.
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