Something that I have seen suggested to be likely under diagnosed as a cause of intestinal permeability (and in the context of also having some degree of autonomic dysfunction) is chronic mesenteric ischemia (CMI). This is something few doctors realise can occur as a cause of only mild GI symptoms, and can occur without having evidence of stenosis of any of the main bowel arteries, chronic non-occlusive mesenteric ischemia (very much akin to what occurs in about 80% of cases of Ischemic Colitis (IC), and most often without the bloody diarrhea that tends to go with IC).
This is where autonomic dysfunction can come into it. Excessive dysfunction of a single blood flow regulator can precipitate intestinal ischemia so anything that can impair your cardiac output and/or regulation (i.e., vagus nerve dysfunction) can also affect the blood flow to the bowel
The intestinal mucosa layer is usually all that is affected, usually only occuring during the digestion process when the physiological demand for extra blood flow can't be met. With this, you might have severe debilitating abdominal soon after eating, or you might only have some mild abdominal symptoms, the latter quite possibly being put down to "just having IBS".
Very hard to prove CMI though as intestinal ischemia periods are very short lived and, as the mucosa layer is in a constant state of self repair, rarely causes any bowel or blood pathology to diagnose it from. There are no other specific tests for functional assessment of mucosal ischemia.
Trying things that can improve the blood flow to the bowel (nitric oxide boosters) can be all that you can do to see what happens. The catch 22 is that having intestinal permeability because of mucosal ischemia can render you intolerant of taking anything that can help with blood flow and for that matter, can be the same for the other usual suspects often recommended for gut healing.
Even if improving bowel blood flow helps with GI symptoms, the intolerance problems can still persist unless or until the cause of intestinal ischemia is eradicated (or fixed if it happens to be a vascular stenosis issue). Not easy to narrow down a cause when autonomic dysfunction is involved.
Clinical management of chronic mesenteric ischemia
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6498801/
[CMI is defined as insufficient blood supply to the gastrointestinal (GI) tract resulting in ischemic symptoms with duration of at least three months.
1 Typical symptoms of CMI include postprandial abdominal pain with food aversion and weight loss. The abdominal pain is classically located in the mid-abdomen or epigastrium and starts usually 20–30 minutes after a meal with a duration of 1–2 hours. Atypical symptoms are constant abdominal discomfort, nausea, vomiting, diarrhea or constipation.
1 Abdominal bruit may be present during physical examination;
however, the “classic CMI triad” of postprandial abdominal pain, weight loss and abdominal bruit is only present in 16–22% of CMI patients.4,
5
Chronic
non-occlusive ischemia (NOMI) or “migraine abdominale”
19 is characterized by symptoms of CMI in the absence of a vascular stenosis and is diagnosed in up to 13–16% of all CMI patients.
10 Several pathophysiological mechanisms causing chronic NOMI have been suggested: underlying conditions such as cardiac and pulmonic insufficiency, shunts, occlusion of smaller arteries due to spasms or micro-emboli, and autonomic dysfunction. Therapy is directed to ameliorate the adverse effects of the underlying pathophysiological mechanism,
that is vasodilating medication in case of autonomic dysfunction or optimizing oxygen supply to the GI tract in case of underlying cardiac or pulmonic disease. Successful treatment of these patients, however, is challenging because the etiology of chronic NOMI is not fully unraveled yet.]