With the PP and the kernel speed the problem is most people can as you have found only get 45KHz reliably, I had this problem but now I have the SS its no longer an issue
Like you I have high count encoders and was using electronic gearing of the drives, i didnt like the cogging at low speeds of anything higher than 2:1 geraing so that meant my rapids were limited to 3300mm/min, with the SS I run it at 10,000mm/min but have had it double that but due to the weight of the axis I have turned back to 10,000 which is still double the original spec of the lathe.
If you ge a SS then make sure you set the drives gearing back to 1:1 as I had some slight positional errors when I was first testing the SS on the lathe, I had left the gearing as I was jumping back and forth between the SS and PP.
Dont think you should have any problems with the BOB but dont have one so cant say for sure and the 6ppr sensor should be fine, the SS can read fast enough to see the short pulse of an encoders Index, something the PP couldnt do.
Hood