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.

Thanks for sharing your use case. Currently there is no way to exclude certain files. There's a separate feedback entry for this at http://feedback.textasticapp.com/topic/107275-filter-exclude-files-to-download/

Tabs will be available in v1.1.

Will be fixed in v1.1.

Will be fixed in v1.1.

The default extension for Markdown will be .md instead of .markdown in v1.1 when you try to save a newly created Markdown file.

Will be fixed in v1.1.