Yes I recall the same reference to (long gone) "color orientation dots" in the shop manual. This presumably was some mark visible on brand new lifters so is of use when assembling engines with new Ford lifters.
I got my manual out now, and I see the figure A 13090-A on page 03-01B-44 of the 1991 Escort Tracer shop manual includes a drawing of a lifter. This shows the color code opposite the oil feed hole into tappet. The instructions say "Color orientation dots on the tappets should be opposite the oil feed holes in the cylinder head."
This would put the holes in the lifters in line with the holes in the cylinder head.
I can't see how putting the lifters in the other way could cause harm.
The drawing has a rather useless label, "color code on tappet" with an arrow pointing to the center of a tappet. Additional gems are ""Install the tappets with the plunger upward"- i.e. don't put them in with the little rolly wheel thingy upward.
I still like putting the oil feed holes opposite the tappet holes, as then the oil will travel around the groove in the lifter, and carry any air with it into the lifter and then out. If the holes are aligned, then there is a dead pocket of oil (and possibly air) in the groove.
On my 1995 engine, I oiled the lifters after disassembling and cleaning them, but otherwise they were empty. The oil filter was also empty, and I guess the oil galleries had drained back completely as the engine made a God-awful clattering for about ten seconds on starting. After that, and on subsequent starts, it was nice and quiet.
With the small Ford V8s I used to run the oil pump with a speed wrench and 1/4" socket on its hex driveshaft, but it's not possible to run the oil pump on the 1.9L engine to prime the oil system, unfortunately.