However, symmetric cryptography like AES or ChaCha20 (assuming that the best-case quantum attack is a brute-force search) only gets a square-root speed-up and thus doubling the key bits actually does alleviate the quantum threat.
My very vague impression of quantum computing is that making a quantum computer with more qbits is quite hard.
They also say later on in the paper that, given certain constraints, it should be possible to use multiple quantum computers with fewer qubits per computer - at the cost of a slight increase in the total number of qubits.
TL;DR: yes, just moving from 2048 to 4096-bit keys will not suffice. But, if you make a composite key out of many 4096-bit keys (such that the key file is now ~1Tb) then then can achieve a reasonable level of security. And yes, I do think the paper is (at least in parts) somewhat tongue-in-cheek!