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or they could have been running far longer than you have and have historic transactions in their mempool.

Yes, before running the instance I let my bitcoin node run for some time until there are some blocks not completely full and I also check that my mempool have more or less the same number of transactions than others like this: https://mempool.observer/

This problem has caused me some headaches as you can see here: https://bitcoin.stackexchange.com/questions/99717/transaction-being-ignored-by-miners-i-mean-ignored-not-not-mined-because-low/99822?noredirect=1#comment113126_99822

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So, the question would not only be: which pool makes the most optimal blocks, but also: which full node implementation and which settings makes the most optimal blocks

As far as I know, Mining with other bitcoin node than bitcoincore is reckless since the consensus code is nothing to mess with. So I'd like to focus in pools not in implentations. Anyway, note that here: https://gist.github.com/Xekyo/5cb413fe9f26dbce57abfd344ebbfaf2#file-candidate-set-based-block-building-md you have a possible improvement over the regular greedy algorithm.

If a mempool is implementing or not a better algorithm is not worthy to know now. But maybe in the future when the fees gets higher.