Yes, we always consider sockets and fill them with the best available gem for all gear rankings on the website.
Best in Bags will choose a soulbind and conduits for you, but you can lock in a soulbind and force the optimizer to use that instead if you wish. To do that:
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Click anywhere on the row of icons representing the chosen soulbinds:
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Click on the soulbind that you want the optimizer to use, then click Lock Path:
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Then click Close, and Re-Optimize.
If you ever run into a case that doesn’t make sense to you, you can always create a snapshot and post it here with your question, and we can take a look at it. Instructions on how to create a snapshot are in this post: