If a player is not willing to suffer the penalties that were agreed upon, then there is no trust.
If there was a misunderstanding as to the interpretation, then it's really up to the player or the GM to define that interpretation as it differs from the RAW. According to the almighty Rules as Written,
"Whatever type of flair the character selects, it must enable
other individuals to easily remember him. Any individual who
attempts to identify, trace or physically locate the character (or
gain information about him via Legwork) receives a +3 dice
pool modifier on all tests made during such attempts (including
Perception Tests)."
What does this mean?
Well, it means that once someone has your number, then finding you is much easier.
Therefore it is conditional on being identified in the first place. This is where disguise comes in. If you are not identified as an intruder, then they're not looking for you. But, once you're busted, you're easy to spot.
Naturally, you'd have to be playing a specific type of game to try and bust into a zero zone with a glowing blue mohawk, but as you and your team gain Rep and, possibly, bounty hunters, it's going to become problematic all of the time.
If it later becomes problematic, then spend the 10 karma per level taken to buy it off. Consider that the cost of going pro.