Realms has an auto-kick feature after 10 minutes. This can cause issues, and not just traditional AFK/AFK Farming things.
For example, it will kick you in the middle of the End Credits.
I think /setidletime should indeed be a feature in Realms, or at the very, very least, an extended period before the auto-kick
Could be related to MC-138670
Now that I've reread and relooked your report, it sounds like you didn't die or drop your tools, so this may be irrelevant
I'm not sure if this affects it, but the Z Coordinate for the Main Overworld portal (209) is closer to 22 (Nether Portal 1) than 18 (Main Nether Portal). Also, though I believe Y Coordinates don't matter as much as X and Z, the Y coordinate for the Overworld Portal 1 (167) is closer to 57 (Main Nether Portal) than 52 (Nether Portal 1).
I don't have too much knowledge on Nether Portal linking, but these coordinate 'differences' may very well be affecting your linking.
There is more or less no information provided.
But.
Items are supposed to float on water, such as a broken dead bush.
If you are talking about dead bushes being placed/generated on top of water, you may ignore this 🙂
I may be wrong, but I think this behaviour is intended to happen.
I do not believe this is a duplicate of MC-123584
I don't believe a torch would be considered a complex model.
When the debug rendering pie chart the warning said to be logged do not get logged when breaking torches.
I don't believe the block changes are resulting in a redraw of the entire chunk section.
If you could kindly unmark this as a duplicate and resolved, that would be greatly appreciated.