(5) This DA/H should take into account any add-on to the published minima as
identified by the operator’s management system
My bold above; this is the root of the issue. Under EASA rules, everything is down to the operator.
If the operator has surveyed every NPA at every arport they operate to or use as an alternate and determined that the obstacles that limit the MDA are not in the area where dipping below during the first stage of a GA would be an issue, then they can use the MDA as a DA. They can even do it on an individual approach basis if they wish, as long as there is a sensible way of publishing what to use for each one, e.g. customised approach plates.
However, only the largest operators have the resources to do this, or even the desire. So the majority just say "add 50ft".
Let's face it, how many times is it actually going to make a difference to whether you get in or not. And if you don't, it's not a safety issue since you still have fuel to divert and land at your alternate with more than final reserve (you do, don't you???).