1. (Design) Building floorplate and architectural complexity (i.e., divergence from 'big box')
2. (Construction) Schedule adherence. Almost any one-off expense to stick to the schedule is worth it, but to your point, these are often challenged or delayed. Building and testing equipment on skids off-site is almost always worth it.
3. (Design/Commissioning) Schedule adherence. For commissioning this is typically driven by design choices (did you pick a high-TRL process, or if not, do all the work required to mature it in parallel to construction?) and by building the right commissioning team (knows their job, knows the plant).
If more expensive plant & equipment gets you ahead on any of these 3, 99% of the time that is an overall optimisation.