I have (hopefully had) a very similar problem with a table not found error when running phpunit. The test worked fine when using my development database (local.sqlite) but failed when I used the phpunit configuration (phpunit.sqlite). Simply trying to have a separate DB for the unit tests.
After alot of head scratching and stepping through the code it appears that the database to be used for tests must be migrated manually once after creation to initialise it BEFORE the tests are run. The DatabaseMigrations trait appears to expect a base migration to exist already before it can roll it back. It does not appear to like a completely empty sqlite file (as created with "touch abc.sqlite" etc.
I set up a config.database with this entry
'phpunit' => [
'driver' => 'sqlite',
'database' => storage_path('phpunit.sqlite'),
'prefix' => '',
],
the phpunit.xml file had these entries
<env name="DB_FILE" value="phpunit.sqlite"/>
<env name="DB_CONNECTION" value="sqlite"/>
<env name="DB_HOST" value="localhost"/>
then I ran
php artisan migrate --database='phpunit'
After this phpunit stopped complaining and all test started to behave.