That's because these routes are archived in .ap files. That's not new, it was the same before TS2015. Just extract their RouteProperties.xml from the .ap file (using 7zip) and RW-Tools will see them.
If you need to find the route folder, start TS2015, Edit, select the route, then click on the "Open" button. This will open the correct folder in Windows.
Further to the above, although extracting the RouteProperties.xml will allow the route to be displayed, you will also need to extract the scenarios if you wish to swap rolling stock in them.
Note that if you use the version of 7zip which you can download from the web, it may leave extracts from .ap files as Read Only.
If you use RW_Tools and select'Find all .ap files' and then select the .ap files you wish to unpack and use the button 'Unpack using 7zip' - this uses a different version of 7zip internally and renders all the extracted files as Read/Write which is necessary for some features of RW_Tools like swapping stock.