I had gone throguh same situation. My Spouse was in Saudi Arabia and I was in Pakistan. We were allowed to submit passports in our countries of residence. This is pretty much possible. Here is what I did :
1- when I got PPR1, I wrote an email to Visa officer explaining my situation and mentioning that it's not possible for me to submit all the passports together. (my experience: if you want VO to reponse your email quickly, address him directly like Dear ABC, MHO.. etc if you know his initials)
2- he replied "I will send you another set of instructions for PPR-1 shortly .
3- after around 20 days, I got another email from him with instructions attached for PPR-1 for Pakistan and PPR-1 for Saudi arabia.
4- I emailed all the passport COPIES and forms together to CHC London and mentioned it clearly that which person wants the visa to be stamp in saudi arabia. (I also add text below each passport copy that person is residing in KSA/Pakistan and will be able to submit passport in Riyyad/Islamabad - This is very important so that VO doesn't mess things up.)
5- I got PPR-2 email for Pakistan and after a couple of days my spouse got it for Saudi Arabia.
and we are now landed immigrants
Please feel free to inbox me if you have any question.