As long as new features are being added, there needs to at least be separate 'release' and 'main' code branches whenever an update is released and there are still things being worked on. Especially shortly after release, there were multiple smaller patches released with bug fixes or minor updates, while larger updates (like the companion DLC, etc) were being worked on. Even the last update, with the compressed save format, Steam cloud support enabled, etc, could not have been released without separate code branches, since work was ongoing with the harder difficulty mode and new skills, etc.

The next games will be built with the same engine, so once the Linux version is brought in line with the current Windows and Mac versions, future engine updates can be done concurrently.