Fix upload properties not overridden by protocol specific ones

[silvanocerza]

Please check if the PR fulfills these requirements

• The PR has no duplicates (please search among the Pull Requests
  before creating one)
• The PR follows
  our contributing guidelines
• Tests for the changes have been added (for bug fixes / features)
• Docs have been added / updated (for bug fixes / features)
• UPGRADING.md has been updated with a migration guide (for breaking changes)

• What kind of change does this PR introduce?

Fixes a bug with pluggable upload.

• What is the current behavior?

Board upload properties that are specific to a certain protocol don't override the default property when protocol is specified.

• What is the new behavior?

Board upload properties that are specific to a certain protocol now override the default one.

Using the following properties:

leonardo.upload.speed=256                                                                                                                           
leonardo.upload.serial.speed=57600                                                                                                                  
leonardo.upload.network.speed=19200 

and the serial protocol would be the same as having the following properties:

leonardo.upload.speed=57600                                                                                                                           
leonardo.upload.serial.speed=57600                                                                                                                  
leonardo.upload.network.speed=19200 

• Does this PR introduce a breaking change, and is
  titled accordingly?

Nope.

• Other information:

Overrides #1420.

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