Have used both for many years, my take use the glass where appropriate ie on lathe the X axis, mill on Y axis possibly vertical as well (Zo)
Magnetic 1 micron for anything else, especially lathe on cross slide. 5 micron will show up on repeatability as in threading, I get errors up to 0.04mm not good when doing .75mm pitch threads on high class products with no play.
Magnetic on mine are 25 x 7.29mm thick rather than C type 40mm thick. Further to that no masses of overhang needing circa 2" plus travel at either end plus having to go next size up. Imagine a tail stock with 4" travel, available size may be 6" plus 2×2" both ends, means unit would be 10" long.
Glass scales will need stripping down and cleaning at inopportune times once per year. Inside the scale its just a 45 degree glass inserted in to an extrusion, nothing more. Just a wipe with a rag.