Why do most URL's have unnecessary '?lang=en&encode=' at the end? Is there any way to remove those?

Can you provide more details?
Where do you see those? What LimeSurvey version are you using?

On every URL in a test survey with one default question and default settings. Latest version 2.65.0+170502.

On every URL in a test survey with one default question and default settings.

Sorry, I don't understand that.

This is what I see - the language, which is a valid parameter, is appended but nothing else.

The language parameter is unnecessary as well. If the default language is English, there should be no need to include that in every URL.

Is there no way to set that and encoding in config and clean up the URLs? I have never seen php scripts set those general default parameters in the URL.

Changing the 'Character set for file import/export' in /admin/globalsettings to '(Automatic)' did not have any effect. '&encode=' still shows up.

I also tried this in .htaccess, with no effect:

RewriteCond %{QUERY_STRING} ^(.*)?lang=en&encode=[^&]+&?(.*)$ [NC]
RewriteRule ^/?(.*)$ /$1?%1%2 [R=301,L]

Related issue: why is index.php in the URL?

domainname.com/survey/index.php/621145

Why not this?

domainname.com/survey/621145

Browsers have no problem finding the right survey with the shorter/cleaner version.

Can I take that unnecessary 'index.php' out with .htaccess? Does LimeSurvey have a 'clean URL' config option somewhere that I missed?

&encode=

is not coming from LimeSurvey. There must be something else going on.