Not meant to be 'violet' either.
To begin with, 'Viorate' has always been the official spelling, as you can see on their official site. It is a fantasy name, one they designed because they thought it sounded neat I'm sure. 'Violet' was introduced by NISA in Trinity Universe, likely because the name looks close to 'violate' and is pretty strange in general. It was repeated by Udon in the translation of the Atelier Series Chronicle, repeated again by Koei Tecmo in later Atelier games (as Violette), before finally settling on the original spelling again in Nelke.
Some Japanese lessons for those of you not as familiar with the language. 'Violet' in Japanese has a few different common spellings, and you wouldn't see much outside of these spellings that often. To go over them:
- バイオレット (baioretto)
- ヴァイオレット (vaioretto)
- ヴィオレット (vioretto)
Japanese doesn't have a V sound, it just uses ヴ to represent it. You'll see a lot of loanwords that use B instead.
Let's compare that to Viorate.
- ヴィオラート (vioraato)
This is not pronounced like violate or violet. Try this instead: vee-o-raht.
This is quite different from your common violet spellings, and I'll explain the nuances of the sounds involved. The difference comes down to レット (retto) and ラート (raato). The ッ character indicates a slight pause, which we represent in English using a repeated consonant. The consonant is not really pronounced at all. The ー character marks a long vowel, which is represented as a repeated vowel.
In Japanese, the presence of these distinctions is actually a big deal. Fudging word pauses or vowel length can greatly change the meanings of words at times. They are similarly used to help Japanese people say foreign words closer to how they are intended to sound.
In short, the sounds involved in making 'Viorate' and 'violet' are quite different, but the change to 'Violet' was likely made because nobody knows what to make of the actual name.