The engine that donated the primer head in question did in fact have the primer higher than the IP. However I would not think this is really necessary, as this primer head does not have an air bleed-off port like factory IDI setups have. My factory 7.3 IDI filter head has its air-bleed port plugged also, I think it's more trouble than it's worth. I haven't yet decided whether to remove the factory IDI filter head or not, that sort of depends on what I do with the primer - the factory 7.3 filter is a 12-micron one, so if the general consensus is the primer should be used with the finest filter (2-micron) there is really no reason for me to remove it, I will instead keep it for its WIF sensor and fuel heater and just plumb the primer after it and before the IP.
I do have a frame rail filter also, it's in a very convenient and safe spot and will remain there. The new primer cannot be used in its place tho, as a) it will be a royal pain to operate the pump there especially in bad weather conditions, and b) the water separator filter that fits said primer is ridiculously expensive while simple filters are very reasonably priced.