From the private thread discussing the issue

protobufjs is big, complex, uses eval and has circular dependencies

Seem like there is even viable alternatives out there https://github.com/timostamm/protobuf-ts

Ideally we won't even pull in the peps here and go with approach @rvagg did in https://github.com/ipld/js-dag-pb/blob/master/src/pb-encode.js