The goal was to use only basic latin letters. But even then - many Slavic languages use or used z for this purpose, none uses x. So why make it arfitically less understandeable? It's not Cxechia it's Czechia.
Historical baggage. The 'c' doesn't contribute to the sound of the czech 'ch' (russian 'x'), unless you read the 'c' as an english 'k'. Kh as in Kharkiv makes more sense.
True. I don’t know much about other Slavic alphabets (other than my own, Serbo-Croatian). It looks like Polish has ć, ś, ź for this purpose. I’d be interested to learn more about the alphabets in Cyrillic. I assume they also have special letters for these three phonemes.