PyConf: Better handling of public tools

As it was found in the Rec!4542 (merged) and pointed out by @graven here, it's impossible for lower-lever python "functions" to check/modify the content of the public_tools passed to the top configure call.

This is an issue since if the algorithm tries to retrieve a non-default Tool instance by name and it wasn't defined in public_tools by end user the Gaudi will create a new Tool instance with default parameters (which can happen silently).

FYI: @graven