Maybe you are completely right, but why than should it not be allowed for some to try, i see no damage except to those who eventually burn money, the risk they knew about in any case.
i was thinking on initial cooperation of say 3-4 nobles, which is not so hard to gain in natural ic way, and if first, hardest step, of colony to would be skipped by such alternative, other elements, food, military defense could have been attempted within week or two after which time success would probably be known.
the main difference - such attempt would not need approval of mother realm and would be sort of adventure. properly played colony takeover is and should be tight vassal relation, this would be alternative.
i would be sad to hear that it is intentional that any new realm has to be largely independent to some of existing ones. to me that sounds only as another obstacle to more competition. new realm would need to have or develop some cooperation rather soon, but would have some more independence initially.
of course, there could be some guys who would go alone and try it, but even that can be rp-ed, i see no damage.
if you are her first neighbor and don't like her, send expedition to destroy her at one. all that can be solved ic.