In terms of why this application might be needed, it could be because of the park's planning application and what is allowed.
Large parts of Alton Towers are covered by a General Development Order (GDO). In short, this means that the park do not need to apply for planning permission to build rides in these areas, so long as they fit with certain, pre-agreed conditions. The park may still submit full plans out of courtesy, or if a part of the application doesn't fit within the existing conditions.
More details can be found thanks to Towers Street:
https://towersstreet.com/features/articles/alton-towers-planning-restrictions/#partfour
Now, Nemesis' location falls within these GDO area. So they would not need planning permission to build something there. But let's have a look at the exact wording of the GDO, from that wonderful TS article:
The GPDO states that the following development is not permitted (in the case of Alton Towers):
In any other case, the height of the building or structure erected, extended, altered or replaced would exceed 5 metres above ground level.
The key words here are "altered" and "replaced".
Say the park want to do a full track replacement, like-for-like. What is the definition of "replaced" in the GDO? Does it mean the knocking down of a structure and putting a new structure in it's place with similar dimensions? Is a like-for-like replacement allowed? What if they keep the supports? Is that then an alteration? What is the lawful definition of an "alteration" anyway?
As an interesting example, Wicker Man also falls under this GDO area, and the park have already done some retracking on that, without the need for planning permission.
It's a bit of a ship of Thesus argument I guess. Say, hypothetically, they replaced one piece of track and one support on Nemesis each year. That would be fine, as seen by Wicker Man. So surely replacing all the track and all the supports at once would be fine too?
I imagine that's what this application is seeking to clarify. It could also be clarifying about any potential noise concerns from deconstruction and construction too.
As for the rumours surrounding a Nemesis retrack. They have been around for a while. To my knowledge, a Nemesis redevelopment has been considered for a few years now, with the park and Merlin acknowledging it was going to have to happen sooner or later if they want the ride to remain reliable and enjoyable. Maybe if Covid wasn't a thing it would already have happened / been underway. It presumably won't be cheap, and will be in lieu of a major coaster (not that Towers needs another new coaster yet anyway imo), so I would expect they would do some additional work (SFX stuff, theming, Sub Terra returns, etc etc) to make it marketable too.