I seem to recall, some time ago, reading an article somewhere on London Overground that said toilets were not required because all journeys are less than 60 minutes. Whilst I cannot find anything online to back this up, if correct, then it would make perfect sense for the entire Northern fleet to be fitted with toilets rather than having a small subfleet for use on the few services less than 60 minutes - and the refurb is the perfect time to do it.
That said, it was also an Arriva commitment to split 24 150/2 sets to create 16 3 car sets and 209 presumably would have been one of them. Whilst it looks to have fallen by the wayside with nothing happening since it was first announced back in 2016, it could still be one idea to be looked at again.