Be explicit about using Protobuf 3 in Scio

[clairemcginty]

Currently different BOMs pull in mixed Protobuf 3 and 4 deps, and 3 wins the dependency conflict. Let's be explicit about which major version we're using in Scio until Beam/GCP BOMs agree on a major version.

See: #5617

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 61.33%. Comparing base (d306bdb) to head (b88889b).
Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #5618   +/-   ##
=======================================
  Coverage   61.33%   61.33%           
=======================================
  Files         314      314           
  Lines       11257    11257           
  Branches      782      782           
=======================================
+ Hits         6904     6905    +1     
+ Misses       4353     4352    -1     

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