Is $T a requirement for your workflow?
Personally I prefer working in frames - it feels more natural.
As for starting at 1001: As oldschool mentioned not every software gives you the luxury of handling negative frames seamlessly like Houdini.
Wouldn't be the first time foo.-89.obj broke a workflow.
Also cut ranges and handles often change over the live time of a shot, again starting at 1001 prevents the numbers to go into the negatives. Unless you offset everything to keep the frame numbers consistent.
Having said that, yes I've seen shots with 15000 frames preroll - everything's possible.
Btw, are you writing a thesis about this, the topic seems quite academic?