Prometheus upgrades follow-up work

[thampiotr]

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Alloy runtime, Prometheus / Loki components and few OTel.

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Prometheus upgrade to v3 was a very large change #3921 that resulted in several issues, as addressed in #4044.

This issue is to track work that is still needed to improve Alloy's Prometheus V3 support and reduce the chance of regressions during other large updates like this in the future.

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