This is mostly a theoretical exercise, extrapolating back patterns observed in Latin loanwords changed after being absorbed and differences between modern dialects.
Brief parenthesis: There are still significant differences in the language within a couple hundred km, to the point where it can be very hard to understand each other. An effort was made during the 60s to define a Standard Basque (Euskara Batua: https://en.wikipedia.org/wiki/Standard_Basque) for education, bureaucracy and law. It is comparable to the unification of Mandarin Chinese at a smaller scale.
Back to the topic of older basque. You have to consider that there's a clear record of the basque living under roman rule, and the region has been under larger powers (but also relatively isolated and autonomous) for its entire history. The intermixing with romance languages started all the way back with original Latin, and the discovery discussed in the article also shows heavy influence from pre-roman iberian languages in the use of their alphabet, even if the languages probably had different roots (iberian is indo-european, basque not).
Nevertheless, the language in this discovery is not really considered basque but more of an ancestor. There is a large gap in the written record, very little has been found between early Roman times and the first writings in modern Basque well into the Middle Ages, at which point heavier intermixing with the rest of Europe started during the 1500s with the pioneering of large-scale whaling and a thriving ship-building economy. It's not really clear when modern basque started, and it has been heavily influenced by other languages pretty much since the neolithic.
I'm not sure actually, I am from Donostia and I did study in Batua and speak it with some minimal Gipuzkoan variations, but Batua is most like my regional dialect anyway, since it is the central one.
But I have friends from inner Gipuzkoa with a very strong accent, and it's pretty hard to understand people from Zuberoa (one of the French provinces) and particularly certain towns and small cities (not always rural) from inner Bizkaia (where Bilbo is).
Not sure how much they stick to Batua in school, but at least it seems like their family and environment has a bigger influence. Of course they understand Batua, and probably always write with Batua spelling, but tend to stick to their regional dialect when speaking.
And no, it is definitely not limited to the older generation.
Durangaldea (Eastern Biscaian part for HN readers) would be hell for you I guess.
On diffs on writting in "Standard" and speaking, Andalusia can be hardcore mode too, specially Cadiz. A Uni student can have a vastly different register on writting for terms at class compared to the day to day speaking.
