It seems to me that your commands are just sequenced wrong, in Python you're performing (examples in parens):

* base64 (ue==) -> decode to binary (0xB9)
* binary (0xB9) -> encode to base64 (uQ==)

whereas in your command line commands you're doing:

* base64 (ue==) -> encode to double base64 (dWU9PQo=)
* double base64 (dWU9PQo=) -> decoded to base64 (ue==)


If we do the same thing on the command line as you're doing in Python, we get:

$ echo "base64encodedvalue==" | base64 -d | base64
base64encodedvaluQ==

$ echo "ue==" | base64 -d | base64
uQ==

$ echo "base64encodedvalue==" | openssl enc -d -base64 -A | openssl enc -base64 -A
base64encodedvaluQ==