Maybe, in today's globalised scientific communication it does not matter anymore.
The native speaker who goes through all my papers before I send them in usually puts everything as "-isation", i.e. BE-like, and I do not mind. Sometimes however, this is a little bit strange, namely when a certain techincal term was introduced in the AE literature first. And yet, I have never insisted on "-ization" instead. After all, from my point of view, there are many much more important aspects about academic papers than the question of BE/AE-spelling.
(And, let me add this, sometimes I think, it might not be that bad in the end to make sure there are some bits of 'European' spelling in your text because international academic life currently does not really benefit from the fact that there is a tendency towards a US hegemony in academic journals. But then, of course, "-isation" instead of "-ization" will certainly not change this to a significant degree. So this clearly is an emotional aspect on my part.)