@A-tan
This is just my speculation, but I think it's because the o sound in Agott would still be closer in english to ア than the possible misinterpretations of a spelling like Agathe. Agathe at first glance, I might mispronounce as "aa-ga-thee". Agate isn't much better either, as the gemstone is pronounce "aa-get". Agott, compared to these two, is closer to "Ah-gah-to". Though it is still a somewhat strange pick compared to just spelling it Agatto.
Olruggio I was really upset with until I realized they were trying to get you to linger on the first syllable to try and replicate the extended u sound in his name.
I can't say I agree with all the official translations, but I understand what they were trying to go for.