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If you feel this is a problem and really want to take the risk running one account over several sites, you can either look into the problem your self. This version is very adaptive and it may not be impossible to wrap an externa plugin around this problem by using one of the many filters/hooks. Besides, if you decide to run the plugin from a "internal orderline perspective", where your plugin is not dependent on the incremental post-id's created by WooCommerce but instead the "long strings" - you could make this work as long as the payment id can be linked to a proper order in a proper site instance.
The problem we stand to with here is that the plugin must have connection with the root network site and know what each site is doing (since the WordPress Network splits up each site in individual tables). It should however not be entirely impossible, but the recommendation is to handle those parts with an own setup. If you feel you want to try that out and you seem to miss important components in the plugin it self, you can create a pull request with a suggested solution for where filters/hooks can be added for this to work. The alternative is to create an issue in one of the public issue repositories and wait for an action - which eventually can be delayed.
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