Relationship of R/S signature in between signed message and DER signature
Bitcoin transactions use DER format for the signature (plus sighash byte), but bitcoin messages use 'plain' format (aka P1363, CVC, PKCS11, Microsoft, JWS and more) (plus recovery byte). The computation of the r,s values in an  ECDSA (which as Oscar correctly commented are not a point) is the same either way, but the data being signed for a message can never be the same as for a transaction so the signatures can never actually be the same value.

Your signature should not be and is not in DER format. The code you link to appears correct:

    $signature = base64_decode($encodedSignature);

    $flag = hexdec(bin2hex(substr($signature, 0, 1)));

    $R = bin2hex(substr($signature, 1, 32));
    $S = bin2hex(substr($signature, 33));


That correctly parses a plain-format signature (not DER), from base64.

    $derPubKey = Signature::getPubKeyWithRS($flag, $R, $S, $hash);


Without tracking down the code this calls, that looks like it should recover and encode the pubkey; whether it also verifies the signature is not obvious.