Fwiw, here is some of my personal understanding & position on decisions to vaccinate or not.
The hypothesis that mmr may be a trigger factor for a small subgroup is ONE possible factor in choosing (or not choosing) vacs. If you have reason to believe your child is in that subgroup of course it is likely to be a sufficiently significant factor for you to base vac decisions on that alone.
There are other factors that may play a part in a decision to / not to vaccinate. These might include (and are likely to be different for diff vacs & diseases):
RISK of disease (dep on further factors inc. where you live, whether your child has other health problems. Another impt consideration here is whether the disease is more serious in childhood or adulthood- if the latter it may inform a decision to vac later on (if the child has not developed natural immunity) so the indiv has immunity when they need it most)
EFFICACY of vaccine
Overlaps with my point above that some vaccines seem to have better staying power than others & some don't seem to 'take' as we'll as others (pertussis for example). The recent Cochrane review of the mmr found no studies looking at effectiveness of Mmr in preventing rubella.
Efficacy of vaccine obviously has implications for effectiveness of herd immunity.
Vaccine SAFETY both short & long term
Some of the newer vacs have not been around long enough for decent long term safety studies.
Given that each disease/ vac may have a different cost/benefit profile for different individuals I am not surprised that there is an overarching policy based on what is best for most people, most of the time.
That doesn't mean we can't or shouldn't, as parents, spend the time looking at the individual profiles for our own circumstances.
Lastly, it is not black & white. It would be nice if it could be recognised that for all if us these are ( and should be, IMO) complex & difficult decisions.
Like many parenting decisions often it is only after you've made them that you find whether they were the 'right' ones or not.