As I understand it these regulations refer to SACs and SPAs [Conservation Areas] and Protected Species. In other words, the regulations are NOT applicable in the vast majority of the UK.
The Regulations have a reasonable and reasoned purpose. They are not imposed across the board to Planning Applications. So in the Due Diligence phase of applying for Planning Permission, we all have the option not to apply in those areas. Or wait.
Or do what they do in West Lancs :
Deliberately, knowingly kill Protected Species in the area a year before applying for PP
Pay the fines for being caught doing so
Form little protective cabals of Local Councillors who can be persuaded to [... ignore ... delay ... facilitate... contest ...]
Fell any number of trees that could be 'in-the-way' and
pay the fines for being caught doing so
Or just BloodyDoIt anyway and cope with the consequences.
Where's my evidence? Read the local papers . Last year, Radio 4 had a particularly interesting program about a local Planning Agency.
We too had an 18 month delay while ecology sorted itself out. Once I had got over my annoyance, those 18 months provided valuable planning time.