In para 2, you state that, " Depending on these findings, ensure any impacts are addressed through mitigation..." and yet it is an accepted fact that mitigation cannot eliminate all the effects of development on the protected area when it is so close to the limit.
The statement in Chap.1. para 1.3 is preeminent at this point: "A competent Authority should only give effect to a plan.... after having ascertained that it will not adversely affect the integrity of the European Site. This means that in the absence of certainty, the plan/project should not normally proceed (subject to the further exceptional tests set out in legislation).

There should also be a presumption against development within the 2.5 km zone unless it can clearly demonstrate through an independent HRA that there are no species affected. If the Developer carries this out, they use their own retained (and sometimes wholly owned) subsidiaries to carry out this work, primarily as a tick box, rather than as a true reflection of the species actually using a proposed site.
This results in Functional land being wrongly categorised as suitable with mitigation.