Enable Developer Mode and then 'Load Unpacked Extension' on the new folder you just created.
Voila. A new version of this extension not under Content Control.
You can now edit, manipulate and manage this extension as you desire. You'll need to click Reload from the extensions area whenever you make a change. Also, you won't receive updates from the original developer. So, you'll need to update periodically and figure out a way to merge updated changes into your separate extension code. You may be able to leave the update_url intact, but it will likely wipe out any changes you make on the next update. This is why I suggest removing it. Though, feel free to experiment.
By leaving the original extension disabled, this will allow you to enable it and periodically receive updates for the author's version. You can then compare the differences between your custom version and the author's version and merge in any necessary changes. I highly recommend this update approach to your new custom extension. If you choose to leave the update_url active, it will likely wipe out your changes on the next update (assuming this even works correctly on a modified extension). Since some extensions don't update very often, this could leave you scrambling to determine what you changed months later when the next update is released.
You will also need to perform these steps on any extension where you want to modify it. Effectively, you're creating a brand new extension using an existing extension's code base and then putting this extension in developer mode.
Note, don't use Mac's TextEdit to edit json files or it will replace " with “ or ” and fail the json syntax check.
Because Google doesn't let you disable the Extension Content Verification feature in any way, your possible workarounds are basically:
Use the canary edition of Chrome, which lets you edit extensions and add your own extensions without any warnings
Copy the extension directory to somewhere else, delete the _metadata folder and load it in developer mode. The drawback of this workaround is that every time you open chrome you will see a message asking you to disable the extension. (because it is in the developer mode)
Prevent Chrome from getting the hashes of the extension, so that it won't be able to verify its content. The drawback of this workaround is that you may not be able to download\update other extensions.
To do this:
Add the line 127.0.0.1 clients2.googleusercontent.com into your hosts file (usually under C:\Windows\System32\drivers\etc)
Clear the DNS cache of chrome or wait a few minutes
Close Chrome and make some changes to the extension
Delete the _metadata folder from the extension's directory (which stores the original hashes)
You can also use an HTTPS proxy server to block only the relevant requests, but that would be too much hacky.