My .02 is to pipe it now when it is easy and brand new. Does the stratification occur in boiler corners? Perhaps, but if piped together and a balancing pipe installed back to the feed, you have covered all the bases.
When you visit a previous installation are many piped together?
No, but remember they are all a bid job, and it costs more and takes more time AND is not a plumbing requirement.....so that may be why you don't see it as much.
Old steam guys were famous for the dual AND balance piping, and probably they knew more than many of us.
I can assure you that when you rebuild a boiler and are pressure washing and cleaning out the internals, there is a sediment layer and packed-in corners where they aren't piped.
Velocity is less, so sediment occurs and over time can be substantial, depending on water quality and chemistry of the source. Do a pH test of the source if you can, and one of the boiler water....that is a good start.
Also, those plugs will come out very easily now, don't think so 30 years from now. Also replace the damned plugs with a nipple and a cap or valve if you choose to not pipe the two together. They should ship them with a 3" nipple and a cap, because anyone who has had to remove an old plug will be very skilled in the 4 letter word category. 'Fire wrench', rotary tools, sawzall, punches, heavy gloves and about an hour per plug on an especially good day. It may look pretty to have a flush plug, but it is a hidden PITA to everyone who works on it.
Koker must be disconnected by now, Dewey, remember to put that boiler in a position so that both ash doors will open when it sits flat on the surface. If we had time it would be mush easier to pour a pad larger than the unit dimensions to keep it dry on the bottom if there were water on the floor. If it's dry, no big deal.
On the boiler drain installed in one side taping: just use 'T' or an elbow that allows 1.5"X3/4"1.5". The 't' is usually much easier to find, but the elbow looks more 'pro.'