Is it standard to be routing out the cavity for these Toneriders? If so, recommendations for techniques/tools for doing so?
It's not the Toneriders, it the factory routing and drilling that's out. Unfortunately this has been a common issue with the many of the TL kits for a long time, and it's frustrating that it's still on-going. If you do need to adjust the pickup cavity, it can be done with a rotary tool (eg: Dremel) and a sanding drum if you don't have a router.
If you need to relocate the bridge holes and don't have an adequate drill press, there are drill guides you can buy or a number of DIY options on YT & elsewhere.
Not sure if your body is also predrilled for a string-through bridge. If so there's help available here for that as well.

I measured from nut to 12th fret and got the 32.4cm. Measuring 12th fret to the saddles was just under 33cm (so I need at least 5mm of play in the saddles, which I just don't think I have).
When setting out your bridge location, you want to measure the entire scale length from nut to saddles, not 1/2 from the 12th fret.

Secondly, the saddle you want to measure to is the E1 (treble) saddle, and you want to position that saddle so there is 1-2mm of thread from the intonation screw visible through the opening in the saddle where the string passes through. (this is for block saddles as shown with your kit).
Now measure the full 648mm from the fretboard-side of the nut to the "break point" of the saddle (where the string will leave the saddle and be free of contact). This determines the required position of the bridge for all the strings to intonate properly.
The treble E saddle will always be the furthest forward (closest to neck) and the bass E saddle will typically be the furthest away from the neck (nut), though there are exceptions with the G string, but that's another subject.