NNNI may test that easily (including the new rundown) while running off the stock 12MHz crystal against the PLL version. A stable canned XO/TCXO would be even better.
An external Osc is certainly easy to try.
TCXO's need care, as some use digital corrections that give small jumps in frequency as the temperature varies.
Some vendors now call their better TCXOs analog compensated - eg
https://ecsxtal.com/news-resources/what-are-the-benefits-of-using-analog-compensated-tcxos/I'm thinking the ideal is
an oscillator that is (very) stable over the integration time. That means long term drift is less important, & it is best to focus to avoid effects like micro-jumps or other disturbances.
The close-in phase noise is looking like the best indicator of that.
A bit of thermal mass around the oscillator can help reduce temperature slope effects, and a local low noise regulator can isolate supply variations.
The 48MHz is needed, however, as you want to upload the binary to the 2040 easily, and you will do it many times, sure.
You just need to be able to generate 48MHz for the USB, so more clock choices exist.
I've not found a very low phase noise oscillator at 48MHz yet, tho NDK say they can cover 20-50MHz in their NZ2520SDA family. Just needs some MOQ
Addit : chip1stop do show a NZ2520SDA 48MHz order code, so I've asked the MOQ on that. (they also have codes for 35MHz and 54MHz, not indicated by NDK ?)