The documentation on dtexec Utility (SSIS Tool) says the following:
/Set propertyPath;value
(Optional). Overrides the configuration of a variable, property, container, log provider, Foreach enumerator, or connection within a package. When this option is used, /Set changes the propertyPath argument to the value specified. Multiple /Set options can be specified.
At first sight this works like a charm but as soon as your value has a space dtexec seems to get confused 
It took me a couple of websearches to find a post that suggests the following:
dtexec /SET \Package.Variables[User::TheVariable].Properties[Value];\”"; space”\”
It seems that this works like a charm 
Because i’m lazy i wrapped this in a powershell function:
function PackageOption()
{
param($name, $value);
"$name;\`"`"$value\`"`"";
}
And now you can use it as following in your deployment script:
$TheVariableOption = PackageOption -Name "\Package.Variables[User::TheVariable].Properties[Value]" -Value "some thing"; &dtexec /File "$package" /Set $TheVariableOption;