Ok but what about the player that increases a couple of his non-career skills but doesn't buy a new spec. Why is he being penalised for adding flavour to his character but choosing not to go completely against his core concept?
This rule is akin to a player hedging his bets and saving up on XP (as it will be refunded) for the point he might want to take a new specialisation. He would actually be better off saving the XP and then buying the specialisation out right if he thinks that he might want to get lots of ranks in those skills.
How is he being penalized? Also, how is buying another spec going against your core concept? If anything not multi specing is self penalizing for flavor, which is perfectly OK but the player should realize what they are doing before making that choice. Several specializations have similar function AND none of them have to be taken literally. A colonist doctor who has made a life long dedication to healing and serving others has many flavor reasons to dip into: both other colonist trees for the extra knowledge and skills, including 2 possible ranks of well rounded which gives access to another 4 total skills; any of the three technician trees, computer use in a futuristic medical field can be highly helpful not to mention the ability to modify/build/invent new medical tech of his own.
AND the player might, I don't know, evolve and grow which might mean they suddenly have a desire to learn piloting. Just buying into the skill doesn't make them a pilot just as merely buying a rank in melee doesn't make you a vibrosword expert.
He's being 'penalized' in exactly the same way the character who doesn't get a discount on the new spec was being 'penalized'. Either not at all (my argument), or by having to pay full price for something based on the cost when he purchased it (the 'get a discount on a later purchase based on when I bought something else' argument).
Take three identical starting PCs, Aurek, Besh, and Cresh.
Each spends XP on 2 ranks in the same non-career skills.
Each now earns 20 XP.
Aurek *doesn't* buy into a new specialization. He has earned 20 XP.
Besh buys into a new, specialization for 20 XP (according to the standard rules). He has earned 20 XP.
Cresh buys into a new, specialization for 20 XP, and gets a 'refund' of 10 XP. He has somehow earned 30 XP (20 earned, plus the 10 refunded).
Either Cresh is being given a *bonus*, or Aurek and Besh are being 'penalized'.