[enhancement] allow mixing of proto and command line based flags

### What's hard to do? (limit 100 words)

Currently mixing options derived textproto configuration file and command line flags results in the following error:

> *__options_proto and other flags cannot be set at the same time

While this is a good practice when options are static value specified by the users, it is inconvenient dynamic path based values usually derived from the environments / build system:
- `dslx_path`
- `output_file`
- `stdlib_path`
- `interface_db_proto`

### Current best alternative workaround (limit 100 words)

Not using proto based configuration and stricly rely on command line flags.

### Your view of the "best case XLS enhancement" (limit 100 words)

Possible solutions:
a. remove path-based value from proto configuration schema.
b. allow-list path-based value to be overriden from flags.
c. define strict precedence rules between textproto and flags options.