There are basically two mods that can remove pedestrian crossings but TM:PE does not change texture by itself and also there is no option to block creating pedestrian crossing for new intersections (there is one for disabling auto-creation traffic lights but crossing texture should be displayed anyways)

Those two mods that can modify road texture and integrate itself with TM:PE crossing feature may also have the option do disable pedestrian crossing by default so it is worth checking their options screen in game.

https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=1758376843
https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=1934023593

HelloMeeze, I have the same problem as you, I was wondering how did you fixed it?