Sure, there are significant security issues. Since when is that a reason to disable a user-originated threat vector? As long as the user in question is informed and alerted to the potential security risks shouldn't it be within the user's purview to decide what to allow and what not?
Even if this line of argument cannot be said for every purpose - and I understand there is a potential for abuse and misinformation about misrepresenting any specific extension - but for instance say Tampermonkey, which the user needs to first download from the webstore then the user needs to also download the script, can't there be sufficient warning that what the user is doing is potentially harmful? Or a requirement from the webstore that Tampermonkey somehow also alert users before loading any remote scripts?
If a user decides to downright download malware we let them (Given, Chrome would block it but you can override that manually) why wouldn't the user be allowed to override these risks (i.e. you can enable it only in development mode etc. with a requirement that such extensions provide sufficient warnings etc.)