Here is how I look at it ...
When my WRX comes in, I'm flashing it to stage 1 right away. Sure, my drivetrain warranty will be gone, but IMO there is no reason that a stage 1 tune should blow my motor .. so if it happens, it would have happened even if I stayed stock. I'm personally willing to gamble, and flash a better tune to try to preserve my motor, because I feel that is the reason for the failures.
I figure if stuff breaks that would have been covered under warranty, I'll just replace it with good aftermarket stuff. Sure, I could get burned and have to replace a shortblock at my own cost ... but I promise you the shortblock I put in there will not blow up at stage 2
If cash is tight for you, and you need that warranty, then stay stock. Just keep in mind that at 60k, the warranty is gone regardless .. I simply refuse to worry about it or worry about "oh what if Subaru denies my claim" .... I say screw em, I'll deal with it myself and replace broken stuff with better stuff.
edit: Forgot to add ... based on what I said above, here is my advice. Ask Subaru if they would replace the pistons and rods in the new shortblock prior to install with some forged ones you will provide. They may allow this, but will tell you that it will then void your warranty ... but DO IT. You will likely have to pay for the pistons and rods yourself, but this is your opportunity to never worry about ringlands again, or have to pay for the labor of install. Just my 2 cents.