Thank you for the solution, I have made some test and found 2 issues.
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“index”: true will not applied to “relation” field, i am not sure kind of this index if will help for the performance, but i used it
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after added “index”: true, when we add/update/delete fields for that model via “Content-Types Builder”, it will shows “An error occurred” when save
So, I applied all the indexes for production manually via command line at the moment until a better solution come out.