Here is a short code that shows how #show: later in #toolbox.side-by-side corrupts the slide titles and slide counter:
#import "@preview/polylux:0.4.0": *
#import "@preview/metropolis-polylux:0.1.0" as metropolis
#show: metropolis.setup
#slide[
= Slide 1
A
#show: later
B
]
#slide[
= Slide 2
#toolbox.side-by-side[
A
][
#show: later
B
]
]
#slide[
= Slide 3
Test
]

Instead of
Slide 1
Slide 1
Slide 2
Slide 2
Slide 3
I get:
Slide 1
Slide 1
Slide 2
Slide 3
Slide 1