If they made a change like this, then of course other numbers and encounters would have to be rebalanced as well.
Most probably they vastly overestimated what they could achieve with their initial budget. SRR was, I imagine, not exactly what they envisioned during pre-production. Backers were a bit underwhelmed as well, so they had to make Dragonfall to appease their fans and secure funding for SR:HK. And they mostly did what people were asking them to do. Do you remember all those posts like "why don't hirelings in SRR have any personality?" Writers and programmers may be different people but they're paid out of the same money pool, and that's why better AI scripts and "biowarian" companions are in direct competitor. We all know what usually wins in the end.
This being said, I hear you and of course I agree. Still, nobody cares about mechanics because mechanics don't sell. Or at least the consensus within the industry is that they don't sell.