Yes muddy clothes gets everything filthy. We used to just whip the leggings down below the knees and drive home , not anymore.I’ve done this too. Stick them on top of my trousers / tights on really minging days for an extra layer. They’re thick and pretty bulletproof. Look shit, but they work!
I’ve been taking a couple of large plastic boxes with lids out with me for the last couple of years now (in my boot). One for clean stuff, and one for dirty stuff. Throw the minging shorts / shoes etc in the dirty box after the ride to save it mixing with the semi clean stuff!