If you happen to go 121 later, it doesn't make much of a difference...But yes, when you're applying for an ATP, the point-to-point time doesn't help you satisfy any requirements.
Don't worry...You'll get the 500 xc greater than 50 miles for your ATP while you warm the right seat for 9 months (a la Great Lakes) to 8 years (a la Comair). It isn't likely that you're going to come out of flight instructing in a piston twin and get hired in as a street captain (in which case you would need to have that 500 of xc>50 nm)
Just to clarify, it is my understanding that you can log any flight time as cross country provided you land at another airport in accordance with the very broad definition of cross country time listed in the front of the FARs. Whether you're operating under 121 or 135 at the time makes no difference on whether you can log it as XC or not.
The differences only matter if you're going for a new rating, cert, or operating privilege and need a certain kind of XC.
The question comes down to what you can apply a certain flight to in terms of ratings or privileges.