Buffett's analogy of bitcoin to checks is completely flawed, even he should know the difference. Notice that he did not compare bitcoin to actual fiat money (fiat money being the most direct form of value transmission) which does have immediate, relative value, but no "intrinsic value" per se.
Buffett hates gold as well, which agrees with his argument of having little intrinsic value, but yet gold dumbfoundedly continues to climb in value relative to fiat money decade after decade. Go figure.
Buffett acts as if companies like Coca-Cola will be with us FOREVER. They won't.
I don't think it's a flawed analogy.
First, let's make checks analogous to Ripple transactions, then compare BTC to Ripple.
Ripple is essentially a more convenient way of passing around checks. In the Ripple network, XRP the on-network currency, was designed specifically to have a low value because the currency is really just there as a transaction 'lubricant,' so-to-speak. The value of XRP needn't be valuable lest it be redundant. It's simply a mechanism that facilitates the transfer of value in the form of IOUs (like checks).
Both the Bitcoin network and the Ripple network serve similar purposes -- to provide a more effective means of transferring value. The fact that BTC as a currency is intended to also function as a store of value (unlike XRP) doesn't necessarily mean anything. Just because something is intended to be a certain way doesn't mean it will actually be best suited for that purpose.
It doesn't matter whether BTC is worth $1 or $10,000 -- the network maintains its purpose regardless of the value of BTC. To this extent, it can certainly be argued that BTC isn't inherently very valuable. Checks, and also the BTC and XRP networks, all serve the purpose of transferring value (or debt entitlement...whatever). All three can serve this purpose just fine without a valuable on-network currency.
Adding my two cents, I think there actually 'is' inherent value in BTC, but this value wouldn't be recognized by Buffet anyway because it's something that's extremely difficult to quantify. To the rest of the world, a socially accepted form of currency that is not dependent upon 3rd-party trust *is* very valuable to many people. Buffet has no need for such a thing.