The closest I know of is WebTIS MixingDeck sites such as East Coast, Southern etc , which after searching allow you to click the tiny "select a route" button on the left, and choose which route restriction on your ticket you want - which isn't quite what you're asking for.
The problem with your example of Aberdeen to Paddington is its not one of the fast journeys into London Terminals - as such the journey planners will ignore it, especially if it can't be completed in one day. It might not even have any valid through tickets (although I'm guessing you are a First employee using staff travel privileges).
National Rail Enquiries allows you to restrict to a single operator under "More options, railcards & passengers", but doesn't allow you to search for a group of operators all owned by the same parent company.
What I'd recommend is using maps to find the rough route you wish to take, then divide this into sections and search for each separately. The maps from
Project Mapping (large PDF - needs Adobe Reader and won't work in some third-party PDF software) are handy as the lines are colour coded by TOC.
At a cursory glance I don't believe there is a route Aberdeen to Paddington only on First TOCs, but there is one into Kings Cross on First Hull Trains. (Aberdeen - Edinburgh - Carlisle - Manchester - Sheffield - Doncaster - Kings Cross)