Does it change depending on aircraft type and/or type of turn that is used to enter the runway?
Yep, aircraft and airline specific.
Is there a Jeppesen reference regarding line up allowance?
It really isnt their business unless they are producing the takeoff data for the airline.
For example we have some runways with arrestor cables built into them, for some aircraft with small tires we displace the threshold to beyond the cables so that the aircraft can taxi slowly over them. As this is aircraft specific its calculated as a line up distance rather than a displaced threshold.
Mutt