I have a linguistics degree and a passion for historical linguistics that will result in me talking your ear off about Indo-European ablaut, so this is probably the first time in my life I've ever been accused of failing to think deeply about language variation / change!

But I do agree with tsunamifury's comment - what you say is interesting, but rather beside the point. What's relevant is a sense of continuity, not whether the modern speakers would understand the original language or not. (I'm unsure why the latter would be relevant at all?) As Benedict Anderson has argued, a nation is above all an imagined community, so what's relevant is that Czech speakers picture a sense of continuity with the speakers of Slavic dialects in 1000 AD, and not with - say - the speakers of Celtic or Germanic dialects spoken at the same time.

(It's worth noting that your example is fairly unrepresentative, by the by. English is a language with an unusually high rate of change (though I'm surprised you went with Chaucer, which many educated English speakers can largely follow, and not something like Beowulf, which no English speaker could understand without training). It's also worth noting that the Slavic languages are languages with an unusually low rate of change, so a text as old as Chaucer would be relatively much easier for Czech speakers to read.)

That is true for Beowulf, but not for Chaucer. If you just read the words in Chaucer, pronouncing them exactly as you would if your were sounding them out, you will be able to understand pretty much the entire thing after at most a few hours practice.

We did this in my freshman English class and it was a lot of fun.