i guess there are a variety of options for this.
I couldn't quite work out if you actually have an SOP for "root cause analysis" or not ? If not, there are several threads here with generic SOPs attached ranging from basic to elegant. Some people must enjoy drawing fishbones.
I tend to use an ad hoc (numbered) Procedure stated to be "based on" a referenced standard method. I then link this number as desired. Auditors like cross-refs. One incidental objective is to minimise the opportunity for an auditor to delve into undesirable nooks and crannies.
In practice (as per yr 2nd query), the applied procedure, inevitably IMO, varies case-by-case when you get to the nitty-gritty. Auditors want to see that you've dug down through the surface and involved (often dragged) in all the pertinent people to get to a "Root".
I append the result of the RCA to a box on the C.action form with details on a cross-linked sheet, which inc. the SOP number. Auditors just love numbers.