Note that the effects do happen in the order printed on the card. So it wouldn't work if they were printed on the other way around. It's simply that the spell all happens before any triggered abilities are allowed to resolve which is why you don't normally notice. You would give the creature a -1/-1 if you used Guile instead of Progenitus, since Guile's effect is a triggered ability rather than a replacement effect.
For example a card that said...
Choose two -
Destroy all creatures.
Counter all spells and triggered abilities.
Destroy all artifacts.
Would stop a Core Prowler's proliferate trigger if you pick the 1st and 2nd mode, but not if you pick the 2nd and 3rd mode.
For example a card that said...
Choose two -
Would stop a Core Prowler's proliferate trigger if you pick the 1st and 2nd mode, but not if you pick the 2nd and 3rd mode.
- Rabid Wombat