Hi, DantianHealth.

Firstly, I would like to sincerely apologize for the delayed response as we have been experiencing an unusually high number of tickets. I am sorry that it has taken longer than usual to respond to your concern and your patience is highly appreciated.

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1. Yes, when we select to Create a MySQL-query-based table by generating a query to WordPress database,

the structure is based on WPDB post types, custom/meta fields, and taxonomies;

while the other option,

Create a MySQL-query-based table by querying a database is a more generic MySQL query generator,

and it has access to more tables in the entire database, rather than just the said WordPress DB tables.

- Please note: this tool is not an ultimate query generator. It simply constructs a suggestion of a query. We are constantly working to improve it, but SQL is such a complicated and flexible language that full automation for constructing queries is next to impossible. 

Consequently, the more complicated the query, the higher is the probability that it will not return exactly what you need. So, you will often need to play around with the resulting query.

Please be advised that writing custom SQL Queries or debugging Queries does not fall under what our support covers.

You can check out this official page of WP codex,  for help with writing custom Queries.

2. In regards to making that JSON data more user friendly/readable;

What you would need to do here is to unserialize the JSON data.

This falls under advanced MySQL, and unfortunately, it will not be covered by our support.

You will have to search for solutions, for example, such as this one from Stack Overflow.

We hope that helps.