If I execute this in Bash
echo \"1 2\"
I get 1 2
. But if I execute
echo \\\"1 2\\\"
I get
After substituting the output of $(command)
back into the command line, the only additional parsing that's done is word-splitting and wildcard expansion. Quotes are not processed, so if the command outputs quotes they will be left in the command line as literal characters.
This is explained in the bash manual section on Quote Removal:
After the preceding expansions, all unquoted occurrences of the characters ‘\’, ‘'’, and ‘"’ that did not result from one of the above expansions are removed.
Since the quotes resulted from command substitution (that's one of the expansions listed before this), they're not removed.