Board Game Arena

Allow for each player to have up to X of 5 or 10 minutes timeouts per game or time played.
This allows for a player to avoid penalties if the person needs to go to the toilet/attend to child etc

Yes, good idea but don't make it the default, just one option.

5-10 minutes of timeouts per player per real time game?

Have you tried the slow Real-Time speed ? For short pauses it should be enough. Else Turn based games let you time for big pauses.

IMO, such breaks wouldn't be relevant for short games (<= 15-20min).
If every player used it, it could triple the length of the game.

Maybe if it was an option you could enable when creating a table, then it would be good.
This would be a nice extra for premium users (who can create premium game tables).

Stalling becomes easier with such a method, especially with shorter games, there may need to be something added to the suggestion to account for that.

Maybe have a system where you can ask for a break, and each player anonymously agrees or disagrees; if anyone disagrees, no break.

This "time out" proposal does not need to be a new feature. It can be accomplished with more options in the existing framework of adding time per each turn to a specified maximum. And obviously this suggestion is intended for longer games, not ones that only last 10 or 15 minutes anyway.

Take Catan as an example. Right now the options in setting up a real-time game are:
Slow speed +1:52 per turn (maximum 6:00)
Normal speed +1:10 per turn (maximum 4:00)
Fast paced +0:44 per turn (maximum 3:00)

The option I'd like to see, in addition to those, is something like +0:40 per turn (maximum 8:00). Because in Catan, most of the time you can do your turn in under 40 seconds but occasionally (the initial settlements at the start of the game, and possibly some endgame situations) you need a few minutes of thinking time. Also, as the OP noted, sometimes you need a few minutes for a bathroom break or to answer the door. The problem with Slow speed is it lets a player theoretically use almost two minutes on every turn which can drive the other players crazy.

(This idea of a fourth option, with a per-turn time less than that for fast-paced but a maximum time "bank" greater than that for slow-speed, might also solve the Ark Nova problem that many people have complained about on these forums.)