Bot is a problematic example, as it has many different pronunciations depending on meaning and region. But non on the common pronunciations have an 'a' (IPA), like Gracias.
True, I was simplifying a bit. Technically "gracias" is /a/ as you point out, while bot is /ɑ/. But /a/ doesn't really exist in General American English, so bot (or bra, as sibling suggests) is the closest on the IPA vowel chart.