When you use SetTimeout in a scenario selenium script it overrides the URL Timeout setting in WPM (set at the bottom of a check's settings)
Having two such timeouts is helpful though, especially in certain use-cases.
Consider a basic example of navigating to Page1 as well as other commands to check various parts of the page exists.
If you use SetTimeout of 60s and load Page1 with 'open' in Selenium. But there is an object on the page which is taking 80s to load (perhaps an ad tag). This blocks DOM Complete and therefore the scenario fails because it exceeded its timeout of 60s.
This produces a horrible alert to say the scenario failed at that first step, and if you're lucky you will find the offending tag in the waterfall.
Importantly that tag might have been low priority in terms of your page. Sure it blocked DOM Complete but the page was rendered and could be interacted with. In this scenario I could have had severity mapping for the domain belonging to the tag provider, mapping this result to WARN instead of FATAL. BUT the fact that I hit SetTimeout destroyed all that because all scenario errors are instantly FATAL.
Consider if URL Timeout still worked (or if one can be custom set in the scenario) and I had it set to 40s. In the same example after 40s the offending ad tag could have been forced to URL Timeout. This would have allowed DOM Complete to happen and therefore the 'Open' command in Selenium would finish. What I achieve here is a working scenario, and the check itself would flag WARN because the URL Timeout on the ad tag would be severity mapped.
Sorry for the wall of text but please look at this because at this moment your tool has made very few strides to work correctly with modern websites that actually have a whole array of tags and dependencies.