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Synchronization
In this plugin, "synchronization" refers specifically to downloading data from iNaturalist to be applied to your Lightroom Catalog.
The iNaturalist API only provides limited metadata for photos, which means that it can be hard to find specific photos within your Lightroom Catalog which actually belong to an observation. Currently we search on the time and GPS co-ordinates of the observation (not of a photo within an observation!), and, if necessary, try to refine that based on crop dimensions.
Many wildlife photographers will shoot bursts of photos, firing off a few photos a second, picking only one of them to show the world. If you keep the alternate (unselected) photos in your catalog, then when you try to synchronize from iNaturalist it will not be certain which photo of the burst is the correct one to tag.
To make things even more tricky, the iNaturalist web interface seems to remove the seconds value from photo timestamps when it constructs observation times. That means that every photo taken within the whole minute becomes a candidate to match.
If you don't have a root keyword set up, then keywords can't be properly kept up to date. When an identification changes on iNaturalist the plugin doesn't know which keywords are safe to remove, and so the "old" keyword won't be removed and you will end up with incorrect or maybe just duplicate (if an identification gets refined from, say, genus to species) keywords. If you do set a root keyword up, the plugin considers any changes within this root keyword to be safe to make.
When keywords are created in Lightroom using the SDK, there is only an option to set whether or not the main keyword is exported; the setting for synonyms being exported is always on. That means that if you choose to set keyword synonyms in this plugin, you will have to change every keyword that is created if you don't want the synonym keyword as part of your exported file. You can edit the keyword by right clicking it in the Keyword List in the library module, Edit Keyword Tag... and then unselecting Export Synonyms.
As you saw above, the limitations of the iNaturalist API make it tricky to find specific photos which match your iNaturalist observations. If you have a collection which contains the photos you've uploaded to iNaturalist you can have the synchronization only search in there to find potential matches. So, if you selected only one out of a burst of photos, you're much more likely to find the right photo to which the plugin can add metadata.
Doubly unfortunately, Lightroom limitations mean that we can only check whether a photo is in a normal collection[^1], not a smart collection, so you cannot use a smart collection for this use. Since this technique is mostly only useful during the initial synchronization (if you use the plugin for publishing as well as downloading metadata), just copying from a smart collection once and then un-setting the preference after the initial sync should be good enough. Jeffrey Friedl's Smart-Collection Sync plugin is an alternative option if you need to keep a normal collection up to date with a smart collection regularly.
As an example of how you might use this feature: before using this plugin I used to use flags to mark everything I would upload, so I created a smart collection for all my flagged photos, then copied those all to a normal collection, and use that for the synchronization. I went from finding only about 30 photos out of approximately 1200 observations to matching most of them. After that initial sync, I went back to the publish manager settings and changed the option to "--".
[^1]: This is not really true. It's just slower to do the check for whether a photo is in a smart collection or not.