Jon this is what I have been saying, but there's one wee point to be added. Had the OP gone straight to the FC it might not have avoided the Council because the FC might automatically consult with the Council on any FL application in a CA. It doesn't have to, but it might.
I believe there has always been a deliberate effort to align the Planning and Forestry Acts so that the need for double applications can be avoided in some situations. I think if the Council had come back within a week of notification and directed the notifier to the FC it would have appeared more reasonable but it still would have been legally wrong to try and prevent the works by doing so. And, after all, what does non-determination really mean? Determination is making a decision on an application, but s211 isn't an application, it's a notification. All we can possibly surmise is that the Council means it hasn't made a decision about whether to TPO or to agree to the works. It might be possible to say that it is not trying to stop the works and is merely being helpful by flagging up the possible breach of Forestry Act controls. Or it might just be hoping to see restocking secured through a FL.
The following generalities can be stated, though (for England).
1. In TPOs a Council consent does not remove the need for a FL. A FL application will result in either (i) mandatory consultation with the Council and, if objected to but otherwise the FC would grant it, will be referred to the relevant Minister to be dealt with under Planning legislation or (ii) referral of the FL application to the Council to be dealt with under Planning legislation. Any consent arising does not require a FL. Thus, a TPO consent only trumps a FL requirement when it has been granted following a FL application. Just to be clear, a TPO consent obtained by direct application to the Council does not trump the need for a FL.
2. In CAs a Council agreement or inaction on a notification does not remove the need for a FL. A FL application does not have to result in consultation with the Council. If a FL is granted no CA notification is required.
The absurdity seems then to be that a FL in a CA could be granted in a way that would deny the Council the option of protecting the trees with a TPO.
And the strange possibility that we have here that a CA go-ahead can only be implemented without a separate FL at 5 cube a quarter and then must stop after 2 years. And a TPO consent can be obtained but could still need a FL or have to be implemented at 5 cube a quarter (indefinitely).