The headphone jack is probably a good option (unless you wanted to use the mute feature) as then you are not putting another bit of circuitry in the signal path, although if the tuner supports "true" pass through then it's a mute point in some ways. You could also just use the MP1 Fx send, IIRC if you don't use the Fx return it doesn't break/interrupt the signal (as it's a serial loop) so it's another spot where you can peel off the signal (pre chorus & master). The HP jack is also slightly cab simmed ie has some top end removed to sound ok in full range HPs (may have some slightly deleterious affect on tuning
), and careful, it's quite high output. However, both of these options are affected by the patch (dist (ODs), eq etc) and the HP out is also affected by the chorus and master vol. I bring this up as in my IPS33 smart shift it has a distortion loop so the harmonizer "tracks" the clean guitar signal but applies it to the distorted signal. Tuning a clipped distorted/eq'ed signal makes it a bit harder to track the note due to the changes in/to harmonic content of the note (very pedantic though, and probably not a worry).
The other way to go with a rack tuner is do the rear jack mod (so it becomes the same as the front input) and go through the tuner first, this could also use the mute feature and will track clean guitar...
I use a Peterson Stroboclip these days, best $75 I ever spent
, strobe & stretch tuning (soo much more accurate than "dead zone" digital tuners) and I can use it to tune all of my instruments.