Whether or not it 'seems' a reasonable route is almost always going to be the primary factor that determines whether or not members of staff allow a particular route, but it unfortunately no longer has a bearing on whether it actually is a permitted route (for which you could obtain compensation if you were refused travel).
As it so happens in your case, going via Manchester on a Leeds to London ticket isn't actually a permitted route, and I can't say for certain whether TransPennine Express staff would be happy with it across to Manchester. What I can almost certainly say though is that it wouldn't be accepted on Virgin, so there's not much point in trying!
It may be possible to obtain an "underdistance excess" from a limited number of amenable ticket offices, which would help you buy the ticket in such a way as that you can use it via Manchester, but most ticket offices are going to tell you that this is "not possible at all" (rather than a more helpful reply of "you don't have a strict entitlement to the excess and my system won't let me sell it to you, but how about X station ticket office?").
