I agree it lines things up right horizontally. What I complained about is that (at least in -ms) a separate EQ-EN pair for each line introduces extra vertical space, so the sequence does not look like a coherent whole. The matrix trick gives a better display, but sacrifices any connection with ordinary math syntax. It makes no sense when read aloud.
Doug Damian wrote: When I try (the non-indented) version of this .S 14 16 .EQ shortid ~ mark = ~ expression1 .EN .SP .EQ longidentifier ~ lineup = ~ expression2 .EN with 'groff -mm', it does exactly what I think you want.