Re: water/fuel seperator
Regarding operation, it does not make a rats *** where the primer ball is mounted in relation to the filter.
But, having the primer ball between the filter and the tank will make it much easier to refill the filter following a filter element change.
Call the filter maker (Racor/Parker-Hanifin for instance) and see what they have to say. I am betting they will say that it won't matter.
Regarding installation instructions, very seldom do the "engineers" write the instructions. Instructions are typically written by technical publications folks. Within a technical publications department there can be differing opinions as to how things should be done. Even within an engineering organization there can be differing opinions.
Take Yamaha for example. For years and years they were saying "no AGM batteries with our motors". People were using them anyway and they worked just fine. Now, after years of saying "don't do it" Yamaha has reversed their position and now say "it is just fine". Same thing with MCA/CCA battery requirements. What once was not OK miraculously is now OK. Even with the same older motors.