Let me try to replay what you're reporting:

   - you are coming from centos to ubuntu
   - you have a clean ubuntu running the packaged version of weewx, with 
   nginx
   - that ubuntu works fine in simulator mode to sqlite3
   - so you want to flip to mysql and run for real
   - but when you put a saved weewx.conf that specifies mysql into place, 
   the system still uses simulator + sqlite3
   - and more confusing, you can manually run weewxd versus the same config 
   file and it does the right thing (mysql)

Yikes....

Only thing I can think of you had a process still running versus the 
old/simulator/sqlite3 file.  Weewx doesn't seem to use the weewx.conf file 
after it initializes (or so it seems from running 'lsof' on my ubuntu 
system).

I'd first disable weewx from starting on boot, and reboot to make 100% sure 
there are no weewx processes running

   - systemctl disable weewx
   - reboot
   - ps axu | grep wee

Then lets start weewx up in debug mode

   - edit weewx.conf to set debug=1 up near the top please
   - systemctl start weewx
   - systemctl status weewx
   - ps axu | grep wee (if you're not sure with systemctl)

If it's running, you should see the debug=1 output in /var/log/syslog that 
should indicate it's connected to mysql, not sqlite3.

A typical ubuntu/sqlite3/simulator output will look like the attached file. 
 Yours should hopefully show something 'other' than 

engine: Using binding 'wx_binding' to database 'weewx.sdb'

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