It's interesting that you suggest that the council has been a custodian trustee for 122 years, as the title was first adopted in the Public Trustee Act 1906. The paragraph about "all sums payable..." refers to the role of the Public Trustee (now the Official Custodian for Charities) at that time.
The current operational guidance from the Charity Commission states that "the custodian trustee holds the title to all the property of the trust but is not involved in the day to day management of the trust."
The governing document of the charity and other legal paperwork will be the key to this, as they may override certain aspects of the legislation. It isn't clear from your comments whether the council has been recording the charity transactions separately and submitting the relevant annual returns to the Charity Commission, but I hope that this is the case. You are correct in stating that the council must now hand over all sums to the charity and a simple resolution will suffice for this purpose. There is nothing to debate.
You haven't mentioned the charity's main asset's nature, but I presume it is a building or land. This should be registered at the Land Registry with the title held by the council "as trustee of..." referencing the charity or the will or deed by which the asset passed to the council. Assuming this is all in place, it is highly unlikely that the council will ever be asked to make a decision regarding the charity, so the issue is unlikely to arise. It is not the role of the council to monitor the work of the managing trustees, and they must not interfere.
Having said all of that, if the managing trustees do ever instruct the council to act, the council should record this as an agenda item at a regular meeting, but any debate regarding the instruction must be limited to the legality of the instruction, not the perceived wisdom or otherwise thereof. The Clerk should confirm beforehand whether or not the charity has the legal power to act, so if it does, the council has no say in the matter. Calling a separate meeting to discuss the charity's affairs will inevitably lead to unwarranted meddling.
Conversely, if a council acts as the managing trustee of a charity, separate meetings should be held, as charity law prevails in that situation.