Tron 2.0/Headscratchers

When the protagonist has been captured by The Kernel and is asked "Who is your user?" Why did he not reply "Alan Two"?
- He didn't use Flynn's gambit of acting like a program.
  - Wait, shouldn't that have been 'Alan 01', not 'Alan 2'?
  - Ma3a repeatedly refers to Jet as "Alan2" Mostly because she thinks that Jet is the next version of his father, Alan. It could be that the system admin played a joke on Jet by making his username "Alan2".
A wee bit of Fridge Horror when playing through again. If Programs are, in a way, the "children" of their Users-Creators, then um...about Mercury and Jet flirting with one another...
- Programs usually look like the person that created them^[1]. Either someone else created Mercury, or Alan has some rather strange secrets...
Another one that could veer horribly into Nightmare Fuel or Ron the Death Eater. It was implied in-game that Ma3a is a cross of Virtual Ghost and Brain Uploading, her programming based primarily on the deceased Dr. Baines-Bradley. Was that accidental, or did Alan do that deliberately?