I am not the author of this plugin but since I have studied the design of this plugin I can answer some of your questions. First, on my installation there are 5 not 4 Magic Fields 2 tables: wp_mf_custom_fields, wp_mf_custom_groups, wp_mf_custom_taxonomy, wp_mf_post_meta and wp_mf_posttypes. These tables contain names and attributes of fields, taxonomies and post types and are essential to the operation of Magic Fields 2. Magic Fields 2 will not work without them.
My two cents:
If you only copy the WordPress tables then there are many WordPress plugins that you will not be able to use not just Magic Fields 2. In particular, two very popular plugins that I use NextGen Gallery and WooCommerce both create their own tables. I believe it is both valid and quite common for plugins to create their own tables.
Having said that I have also studied the design of two other WordPress CMS plugins, Pods and Types, which have similar storage requirements to Magic Fields 2 and neither of these plugins create additional tables but instead store the information in the WordPress tables wp_options, wp_postmeta and wp_posts. So it is possible to make a CMS plugin without creating additional tables. Furthermore, in addition to the difficulty that the additional tables are causing you I have found post copy utilities such as Duplicate Post and Post Duplicator cannot work with Magic Fields 2 as some essential field data is stored in non WordPress tables which a generic plugin cannot know about.