[Maerlyn]

well, this is the way I handle it:

if you choose Hardly industrial every SY will build 2500, enough for lvl 3. (but I usually dont choose HI)

instead I try to get to min lvl 2 and applied research lvl 2 pretty fast, focusing on these facilities to be build (instead of the lvl 1)
before I research lvl 3 of them I try to research the upgraded SY (prefered both levels at once, so I only need one upgrade per planet, but that might be too expensive sometimes.) this means I research lvl 3 res and mins pretty late, obviously.

If I somehow get lvl 3 earlier (through tech trade -> minerals, or through ruins) I do the following.
I usually play with an construction rate of 120% so I only need 100 mio pop on every planet to build them in one turn. if I am able to distribute this population in time I build the SY first, and then build the lvl 3 facilities. if I am not able to get the necessary pop amount to that planet I dont build a SY, but build lvl 2 facilities instead. I build my SY in the end and then upgrade the facilities. usually I start building lvl 2 fasc. and 5 turns before my transport arrives I start building a SY. (however, on small planets its usually smarter to build lvl 2 facilities.)

in anyway, forget the upgrade all button as soon as you research lvl 3.