I think my confusion was driven by:
1) Some parts of Archetype can never be chosen until after career has been chosen (e.g. Natural picking 2 non career skills to receive their 1st rank)
2) RAW says 'begins play with' which suggests a more natural place is the Step 7 (when buying Gear), or even later (i.e. immediately prior to play starting)
I guess the maximum XP Spend difference will come from a Cyborg taking Enhanced Reflexes (+1 Coordination, +1 Vigilance). Assume these are both Non-Career skills (and that we are sticking to max 2 skills ranks at end of character creation) then getting to 2 ranks in both these will cost either:
a. Costs 30 XP if Enhanced Reflexes provided the 1st ranks (2 * (2*5+5))
b. Costs 20 XP if Enhanced Reflexes provides the 2nd ranks (2 * (1*5+5))
10 XP might not seem huge - but given the benefit from some Characteristic increases are only felt at Character creation (e.g. wound/strain thresholds, and Soak) if feels like a reasonable difference.
I'm probably being over sensitive to this... but I've never run a Genesys system before & will have some analytical people in the group who will spot this! (Programmers and Actuaries...)