Without wanting to get embroiled in this debate, it is 100% personal after all! I can’t let this slide…
It’s warmer, you’ve got pockets to keep stuff in, the shorts keeps the crud off you and apart from anything else it makes things a lot easier when you get home as you can ditch the muddy baggies at the door and head to the shower with some semblance of decency without treading god knows what into the carpet.
Warmer? No, unless you’ve got waterproof baggies on (such as the Alp X ones, which are not at all baggy!) an extra layer of sodden material flapping around your thighs is not warmer.
Pockets? If you don’t mind things bouncing around constantly, otherwise jersey/jacket/bag is more sensible, you’re less likely to land on them too!
Crud off? Well it puts it on a different layer of fabric, not much else
Treading crap into the carpet? How do you figure? Your thighs/arse may be slightly cleaner, as they will be if you take your tights off and have lycra shorts underneath. Seeing as my lower legs tend to be as muddy if not muddier I fail to see any advantage there!
I used to use Alp X shorts, they wore through after 3 winters, last year I didn’t bother and didn’t really notice a massive difference frankly. I probably don’t use the MTB that much when it’s stupidly muddy though.