I did notice the comments on UKAR Clive.
I don't think any of these are show stoppers, it will probably end up with approval with the points raised listed as conditions to be met before construction commences, that is quite common. I has a similar situation a several years ago when I designed a golf course, it was passed on appeal but with various conditions placed on the approval all that had to be met to the satisfaction of the authority before construction could commence.
the bigger impact will more likely be on cost - all the investigation will cost money, some of it is specialist work so the provider is in an advantageous situation and any changes to the design are likely to push the cost up. What effect that will have on any sponsor for the construction I don't know but it may commit them to a higher budget than they expected. The cost of the investigations and reports etc may need to be borne by the Trust - bang goes some of the name plaque scheme monies earlier than expected!