It makes pretty good sense to me....
If the Spider (or full jump capable 'mech) makes use of it's jump jets, it can get the same THM if it jumps or if it runs.
A 'Mech like the Jenner can't get the same THM's when it jumps as when it runs because it doesn't mount the full allotment of jump jets in TW. Because of how the mods work in AS, if you left it as a 5j unit, it would get the same mods as if it used it's walking ground speed (which is now considered to be it's maximum speed,) which doesn't happen in TW (aka, when the Jenner runs flat out, it generates a +4, and when it jumps it generates a +3; conversely in AS, when it uses it's ground movement, it generates a +3 on the ground and jumping generates a +2.) So to make it more accurate to TW, the Jenner (and other 'mechs that don't mount maximum jump jets) takes a penalty to make it feel more like it would in TW rules.
Part of the hang up I believe is also that most of the movement mods were lowered (aka, my Phantom OmniMech that tends to ALWAYS have a +4 to hit in TW now only pulls a +3, with the trade off being I can "stand still" and still get that modifier.) The Jenner's possible +4/+3 mods were lowered by one in the conversion. If there's another 'mech that doesn't mount full jump jets that seems to come out better, it's probably how the math worked out *shrug*