Certain practicalities (like "motivating miners of the meta-chain") aside, monoculture is admittedly very comfy.
However, non-monocultural settings are less susceptible to exploits and systemic failures of design.
True. Alt chains would have to have some kind of funding system. The timestamp chain would have a single merkle root. Alt chains which pay more are placed nearer the top.
Miners would merge miner lots of alt chains at the same time, placing the ones which pay more closer to to the top (assuming the protocol rules give better rewards for doing that).
Speaking of which, it would be nice if bitcoin supported unbalanced merkle trees. This would allow much faster updates for the extra nonce.
Or, for a more obvious example, consider the response of people who already bought ASIC units to a hypothetical PoW change

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The timestamp chain could still be based on sha256.