The function of the pelvic floor is what you, as a physiotherapist, are addressing during the session. Bowel and bladder functions can be closely related to the integrity of the musculoskeletal condition of the pelvic floor.
If you are doing your due diligence during an assessment and asking questions about the frequency of bowel and bladder elimination to assess the pelvic floor, then it does seem reasonable.
If you have highlighted a problem and suggest fibre intake to improve the patient's bowel motility, you should assess the risk of the recommendation. The risk is there could be another medical condition that you do not have the competency as a PT to evaluate thoroughly.
A physiotherapist cannot diagnose a patient nutritional issue. Of the scenarios in question, the most problematic one is the prescription of the specific elimination diet. It is essential that results from a prescriptive diet are not interpreted by a PT as a nutritional diagnosis.
A physiotherapist should work with an MD or an RD to help guide a patient's care who is living with chronic diarrhea, as this is not a physiotherapy diagnosis.