I think the only downsides to developer mode are theoretical and one practical.

Developer mode does a few things, including opening ports that are otherwise closed and running the Nova Com client on the Pre.

The first may or may not be exploitable for gaining access to your phone. The second doesn't matter if you only connect with your computer that has the driver loaded. However, if you try to connect to other computers to use the USB drive feature of the Pre, that OS will attempt to load drivers for the Linux NovaCom device it sees before you select USB mode. This is a minor annoyance.

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