The official way to disable the popup seems to be like this:

Pack your extension (chrome://extensions/, tick at 'Developer mode', hit 'Pack

extension...') and install it via drag-and-dropping the .crx file into the
chrome://extensions page.

(Since the extension is not from Chrome Web Store, it will be disabled by default.)

Then for Windows:

In Chrome, go to the Extensions page (chrome://extensions)

Check the Developer Mode checkbox at the top
Scroll down the list of disabled extensions and note the ID(s) of the extensions
you want to enable. LogMeIn, for example, is ID: nmgnihglilniboicepgjclfiageofdfj
Click Start > Run, and type regedit <ENTER>
Under key HKLM\Software\Policies\Google\Chrome\ExtensionInstallWhitelist (create it
if not exists), create a new string for each extension you want to enable with
sequential names (indices), e.g. 1, 2, ...
Enter the extension ID(s) as string values in any order. For example, there is a
string with name 1 and value nmgnihglilniboicepgjclfiageofdfj
Restart Chrome
That's it!

Note: When you update a whitelisted extension, you do not have to follow the same
steps since the ID of the extension will not change.