That message could be clearer. My informal answer would be: "Most likely 'Yes', but if you encounter any problems, don't ask WhatsApp for help."

I'm running a Xiaomi Redmi Note using Mokee (non-rooted) instead of the official MIUI 7. It works perfectly. I just get a notice that WhatsApp is not supported on custom ROMs upon installation. But, no problems after that.

"Your messages will not be protected with end-to-end encryption." This sounds clear, but is it correct?

I'm so sorry. I overlooked that part. That was a big mistake on my part.

You might want to ask on the StackExchange or on https://www.xda-developers.com/ if there is a workaround to WhatsApp encryption on custom ROMs (in case you don't get an answer here).

Although, I'm not sure you should be using WhatsApp for secure messages to begin with: https://news.ycombinator.com/item?id=13389935