It's a worry because health professionals need a full skill set! Women do still have - albeit in small numbers - natural third stages and vaginal breech births. Midwives who have inadequate experiences of these things are not safe practitioners.
"but I think there must be proof to show it's generally better overall because birth with intervention costs the system a lot more and so wouldn't it be better to keep it 'natural' if possible?"
I think what's happened isn't that health professionals are always delivering evidence based practices, but that there is a massive amount of defensive practice, and that the fall out from this is very high rates of birth injuries and traumatic births involving instruments and emergency surgery.
The RCOG did an audit of outcomes at different hospitals where they adjusted the figures for the particulars of the hospital to allow those reading the audit to make meaningful comparisons of the data.
here
The average rate of normal birth for first time mums in the UK (that's birth which doesn't involve induction, instrument or c-sections) is 44% (it would be much lower than that if they extended the definition to include labours which don't involve augmentation with syntocinon or a managed third stage). But you can see from that chart that in some hospitals the range is from 32% to 62% - and those figures are adjusted to take into account the demographic using the hospital.
For third degree tears for first time mums the range is from 2% to 9%. The hospitals at the top and bottom of the range both have similar c-section rates.
For induction the range is 43% to 16% induced labours for first time mums.
In other words there are widely differing practices at different hospitals, suggesting that there are other factors than NICE mandated evidenced based recommendations affecting clinical decision making and birth outcomes.