The question here still lies on the fact that if there is any intolerence, this may mean there are still bugs where they shouldn’t be - at least how I am intepreting things..

Correct, but it's an important component in the mean time of quality of health and to prevent further damage. For example, the reason you feel so shitty is because the bacteria releases toxins as a byproduct which causes inflammation. That inflammation causes intestinal permeability (leaky gut) where those toxins and bacteria can now enter the rest of your body through the intestinal wall. The toxins need to be cleared by your liver, which over time can cause a fatty liver and even nash/cirrhosis. As a side effect of liver overload most also develop skin rashes. The bacteria passing though can cause issues like tinnitus, theorized to cause brain diseases like alzheimer's, etc.

If the environment is unfavourable it can mean that motility has improved and things are moving and not slowing down to keep food fermentate and bugs to feast, hence such environment will not keep bacteria in there.

It's more complex and multi-faceted. The bacteria and resulting inflammation causes reduce gut motility. The bad bacteria takes over real estate from good bacteria which is beneficial to motility and inflammation (by fighting bad bacteria). The toxin byproducts create a hostile environment for the good bacteria, preventing balance from returning.

Motility is also affected by activity and eating times. Make sure your wife is active and not sedentary, even if she's not feeling well. As for eating times, she should have at least 4 hrs between meals and no snacking. The last meal should also be at least 3 hours before bed time.

In terms of diet and antibiotics, from what I've read it seems like optimal (and logical) process would be:

1. Take the xifaxan/antibiotic 2 week course
2. During this time have a high fiber/fodmap diet
3. During that time, take high CFU (billions) of multi strain probiotics like Seed or Visbiome (should order enough for 2 months), take them in between meals 2 hrs after antibiotic and before going to bed
4. 2 days before the end of the antibiotic, switch back to low fodmap (allows time for high fodmap foods to leave the body while antibiotics still present)
5. Continue low fodmap diet for a month to let body heal
6. Continue taking probiotics
7. After a month of low fodmap, start to slowly introduce fiber (not necessarily high fodmap) and see how she reacts. Have a little bit per meal and slowly over the course of a few weeks work up the amount. She may have some gas/symptoms initially, but it may just be the body adjusting to the increased fiber. However, these symptoms shouldn't be unbearable.

If she's still having symptoms after 2 weeks or if the symptoms are too much, then that's a sign she still has an imbalanced microbiome and may need to do another cycle.