Hi,
When using ls:env:configure, I've noticed it's impossible to set a variable to a value starting with a dash, like '-1'.
This is caused by a known Symfony Console issue (symfony/symfony#3624), and the solution should be fairly straightforward to implement.
I would make a pull request, but I think you just need to change one line in lib/n98-magerun/modules/LimeSoda_EnvironmentConfiguration/src/LimeSoda/Environment/Configure.php where the config:set commands are executed (line 38):
$input = new StringInput('-- ' . $command);
instead of
$input = new StringInput($command);
The '-- ' makes sure no argument values after its appearance are interpreted as option names.