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This is exactly what it is supposed to do. "Main site database only" generates a SQL file. "All site databases" on the other hand generates a JPA file. This is documented.

I'm sorry, but you are still mistaken. Ever since the "Site database only" feature was implemented in 2007 (a bit more than eleven years ago) it was generating a .sql file. This is the only backup type which does NOT generate an archive format. This has been very clearly documented ever since. I know because I wrote the feature and its documentation myself. Please let me paste the documentation for you:

Backup Type

It defines the kind of backup you'd like to take. The backup types for Akeeba Backup are:



1. Full site backup which backs up the Joomla! database, any extra databases you might have defined and all of the site's files. This produces a backup archive with an embedded installer so that you can restore your site with ease. This is the option 90% of the users want; it is the only option which creates a full backup of your site, capable of producing a working site if everything is wiped out of your server.



2. Main site database only (SQL file) which backs up only the Joomla! database. It results in a single SQL file which can be used with any database administration utility (e.g. phpMyAdmin for MySQL, pgAdmin3 for PostgreSQL etc) to restore only your database should disaster strike. This option is recommended for advanced users only.



3. Site files only which backs up nothing but the site's files. It is complementary to the previous option.



Warning

Having one "main site database" backup and one "sites files only" backup is not equal to having a full site backup! The full site backup also includes an installation script which, just like Joomla!'s web installer, allows you to effortlessly recover your site even if everything is wiped out of your server. It acts as the glue between the two pieces (files and database).



4. All configured databases (archive file) which creates an archive file containing SQL files with dumps of your main site's database and all of the defined multiple databases. The database dumps can be restored by any database administration tool (for example phpMyAdmin for MySQL). The difference to the second option is that it produces an uncompressed SQL file and doesn't include any extra databases which you might have defined.



Note

Extra - or "multiple" - database definitions are only available in the Professional edition of the component.



5. Incremental (files only). This is the same as the Site files only option, but instead of backing up all of your site's files, it only backs up the files which changed since the last time you performed a backup. The only comparison made is between the file's modification time and the last successful backup's time. The "last successful backup" refers to the last backup made using this backup Profile and which has a status of "OK", "Remote" or "Obsolete".



Restoring an incremental backup set is a manual process. You have to manually extract the files from your "base" backup (an archive made with a Full Site Backup profile), then extract all incremental archives on top of it. Finally, used this collection of extracted files to restore your site. This process should only be used if you really know what you are doing. Do not trust that Akeeba Backup can sort out the collection of incremental backups and help you restore them. It won't.

Since it's a .sql file it is by definition NOT an archive file, i.e. it does not contain other files inside it. That's why you cannot "extract" it with Kickstart. Kickstart extracts the files from inside archives.

As with all .sql files you can only import them with phpMyAdmin, MySQL, Adminer, BigDump or a similar tool. The entire reason this backup type exists is that sometimes people want to transfer just the database and use one of these tools. I have written that in the documentation (see above).

If you no not want to use phpMyAdmin etc then you need to configure your backup profile to use the "All configured databases (archive file)" backup type. This creates a .jpa, .jps or .zip archive which includes both the database dump and the restoration script, exactly as documented.

Please read the documentation I pasted above.