If I recall correctly, okteto manifest doesn’t support local envvars.
One thing I usually do is to create the temporary file with the envvars interpolated with something like
envsubst < okteto-manifest-with-envvars.yaml > okteto.yaml && okteto up
This will replace the envvars from okteto-manifest-with-envvars.yaml with the values you have defined and dump it into okteto.yaml so that then okteto up picks it up