We do seem to be talking past each other.
Broken down, Super-Speed is Speed (1pp/rank) + Quickness (1pp/rank) + Improved Initiative (1pp/rank) + Array (2pp/rank). That totals up to 5pp/rank.
In Hero Lab, if you add an alternate power to Super-Speed, it follows the parent cost of the power (5pp/rank) not the Array cost (2pp/rank). Again, the Core rulebook is a little fuzzy on the issue, but it seems explicit to me that UP says all powers should be no more than 2pp/rank. Yes, you may purchase a Special Alternate Power for free that is also limited to 2pp/rank, but all other powers are similarly limited, they just cost 1pp for the alternate power feat.
From the Core book:
You have Quickness (see page 96) and Speed (see page 100) equal to
your power rank and a +4 bonus to initiative checks per power rank. You
also gain one of the power feats below at your power rank (choose one
when you acquire Super-Speed). You can acquire the others as standard
power feats.
Emphasis mine. It goes on to list suitable alternate powers such as Air Control, Burrowing, Deflect (slow/fast projectiles), Strike, Stun, and Suffocate. All of those powers are 1pp - 2pp/rank which leads me to believe even in Core alternate powers should be limited to 2pp/rank.
But like I said, UP is more explicit:
Effect: Array, Quickness, Speed
You have Quickness and Speed effects equal to your power rank and
a +4 bonus to initiative checks (essentially one rank of Improved Initiative) per power rank. You also have a Super-Speed Array of effects you can do (2 points per rank in the Array). Choose one of the following Alternate Powers, acquiring the others normally (for 1 point per Alternate Power feat).
Recommended alternate powers are:
Air Control (2pp/rank) at Super-Speed power rank.
Bullet (basically Blast, 2pp/rank) at Super-Speed power rank.
Deflect (fast/slow projectiles) (2pp/rank) at Super-Speed power rank.
Rapid Fire (blast with autofire, 3pp/rank) at 2/3 Super-Speed power rank.
Sonic Boom (3pp/rank) at 2/3 Super-Speed power rank.
The list goes on, but not one power costs more than 2pp/rank without having to reduce the ranks of the power below Super-Speed. That to me means that ANY power you choose to add to the Super-Speed array is max cost 2pp/rank, whether it's the free special alternate power or the standard ones.
Super-Speed is special in that it is a container that also has an array. So the Super-Speed effects (speed, quickness, improved initiative, + 1 free alt power) are all usable apart from the other alternate powers in the array. A Speedster will always be able to move and attack or move and throw up protection without having to worry about switching the array only once per round. The container is not the array, it provides an array. Therefore, alternate powers should not follow parent cost. If I have Super-Speed 10, I should not be able to purchase a 50pp alternate power, only a 20pp alternate power. The array is separate from (but linked to) the Super-Speed container.
Make sense?
If I'm still not making myself clear, then check out
this link,
this link, and
this link in the Official Rules Questions at the Atomic Think Tank. They show that Super-Speed is a container of effects linked to (or wrapped around) an array and that array is limited to 2pp/rank.
The only way someone should have a 50pp alternate power for Super-Speed is if they bought Super-Speed 25 (not Super-Speed 10).