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I kind of worry about the same issues regarding phpmyadmin, which is a problem with running any web frontend for a backend as a web app.

Wouldn't a solution like pgadmin3 or mysql workbench be a more secure program across the board?

Preferably you would run this inside your own/company network, and whitelist any domains that will be accessing the web frontend from the outside.
Doesn't that seem a little insane when you can just use an ssh tunnel via any of the desktop apps? I can maybe understand this in the context of a phone or tablet, but the thought of doing any DBA on a mobile device is a little horrifying.
Sometimes a web app is preferable, for the usual reasons, no installation, platform independence etc.

In terms of security it should be no different since you would run this over https.