A lot of new very important papers in i.e. machine learning, quantitative finance come _after_ being implemented in computer code. I just looked at some, and they already seem to use 0 index for the initial states / base layer... here's just one example, where 0 and 1 based indexing is mixed, but I see it everywhere:
In mathematics 1...N is a perfectly good notation. Julia expresses the same idea with 1:N. This is consistent with spoken language (1 denotes the 1st element). Consistency, if anything, would not come down in favor of the software engineering choice here.