Yes, Portuguese, just like English, Spanish, French, German etc. is just one language and as such can be understood in any Portuguese speaking country. However, there are variations in the use of the language, both spoken an written, from country to country just like what happens with the other languages. And people tend to dislike the variation they aren't used to, since it feels "unnatural". For instance, in quite a few cases pt-PT and pt-BR use different words for the same term in English - a "file" is translated as "ficheiro" in pt-PT and "arquivo" in pt-BR (both long established Portuguese words) and "mouse" has been translated to pt-PT (as "rato") and simply borrowed from English in pt-BR. There are also different expressions/idioms, etc.
There is another aspect, though - orthography, particularly related to consecutive consonants. As result of the natural evolution of the language in each country, many words with consecutive consonants (like "actual" and "know") have lost their first of the two consonant sounds (and in many cases that consonant was dropped in the writing). But mostly it didn't happen with the same words in both countries - natural evolution runs by itself. Trying to avoid of this (there are other similar but less obvious issues), at a certain moment the Brazilian and Portuguese governments have decided to set a "common orthography" (in fact, for political reasons related to the status of the language in the UN and other IOs). And exactly because many of the dropped sounds weren't in the same words in both countries, the so called "common orthography" became more a "messy orthography" than a common one.
On top of this, Angola and Mozambique, the two big Portuguese speaking countries in Africa, regarded all this as a Portuguese-Brazilian affair. Besides, they still have a large population with poor formal education (who would have a hard time adapting to orthography changes) and being developing countries probably have other priorities, including because of the spending a change of all school books, for instance, would imply. Hence, they've kept the Portuguese orthography that was in place prior to the change.
Because of all this and of the poor quality of the orthographic agreement, even in Portugal (not sure about Brazil), many people, including scholars, keep using the previous rules.
So, a long story just to tell you that users of pt-PT and pt-BR aren't very fond of using "unnaturally" written texts, and that the two big Portuguese speaking countries in Africa still follow the previous orthography rules, which made me think of using the "pt" locale to cater for them and the pt-PT for the new orthographic rules (these do not solve all the differences of the ficheiro/arquivo type and others regarding to pt-BR).
I can understand your concerns, of course, hence I'll leave it to you to decide whether you want to deal with an extra locale or not. My intention is to keep updating my translations according to the evolution in the English originals, but this is not a promise, of course - no one can rule the future, not even his own.