This was actually a change in Mountain Lion for apps that support iCloud. Other iCloud-enabled apps like Apple's TextEdit, Pages or Numbers or third party apps like Byword and iAWriter have the same behavior. 

Here's the relevant part of the Mountain Lion AppKit Release Notes (https://developer.apple.com/library/mac/#releasenotes/Cocoa/AppKit.html#//apple_ref/doc/uid/TP30000741):

NSDocument Support for iCloud
In 10.8, NSDocument-based applications with a ubiquity-container-identifiers entitlement gain new functionality and UI to facilitate iCloud document management.
When iCloud is enabled and an application is first launched or re-activated and no windows are visible or being restored, instead of creating a new Untitled document, NSDocumentController will display a non-modal open panel showing the user's iCloud library. From there an application can either open an existing document from iCloud or the local file system, or create a new document. 

You can press Cmd-N to create a new document even when the open dialog is shown.

There's currently no auto-format functionality in Textastic.

You can find all existing code completion definitions (JSON files) that are included in Textastic at https://github.com/blach/Textastic-Customization/tree/master/CodeCompletion

If you want to modify code completion definitions, you can edit them and put them in the "~Library/Containers/com.textasticapp.textastic-mac/Data/Library/Application Support/Textastic/CodeCompletion" folder mentioned above. Textastic will pick up the changes at application startup time, so you have to manually quit the app. 

If you do not change the uuid, your custom file will be used instead of the built-in one with the same uuid. If you use a new uuid (you can generate one with the uuidgen command line tool), the code completion file will be loaded in addition to existing ones.

I'll consider changing the behavior or adding some options.

Thanks for letting me know!

Well, Textastic uses Auto Save that was introduced in Lion. That's the standard behavior in modern Mac apps.

Can you configure Transmit to ask before it uploads changed files? 

If I disabled Auto Save, other features like Versions and iCloud would be disabled, too.