I think that's the right way to think of it, Tim. Filters don't care if there is a sudden influx of nasty stuff... if your filter is designed for backcountry use, it should be fine for any conditions. I would guess the only real issue is that all the run-off also raised turbidity, so you have more schmutz in the water to filter out (and that can shorten the life of your filter... if you have time, let the source water settle out first).
About half a lifetime ago Nancy (MrsDrewKnight) and I spent a year in Asia with a first-generation FirstNeed filter. It was a daily chore to pump a couple litres of water, wherever we were, every morning to support drinking, tooth-brushing, etc. We drank water in some very dubious places and never had an issue (though we did have a few food-borne lower-GI parties). The only thing we ever encountered that the filter just couldn't deal with was "glacial flour" from the Everest valley... glacial till ground so fine and suspended in the water, the filter didn't take it out, and it wouldn't participate over the course of a day. The nurse we were with at the time said it was not an issue, though, and we survived unscathed.