Allow passing of options to Tools in onsite scripts, fix flatfield overriding config

[maxnoe]

Fixes #1040

[codecov]

Codecov Report

Base: 71.65% // Head: 71.64% // Decreases project coverage by -0.01% ⚠️

Coverage data is based on head (a0a0da6) compared to base (4f7e9ec).
Patch coverage: 66.66% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1042      +/-   ##
==========================================
- Coverage   71.65%   71.64%   -0.02%     
==========================================
  Files         120      120              
  Lines       11301    11303       +2     
==========================================
  Hits         8098     8098              
- Misses       3203     3205       +2     

Impacted Files	Coverage Δ
lstchain/scripts/lstchain_data_r0_to_dl1.py	83.52% <50.00%> (-1.00%)	⬇️
...site/onsite_create_calibration_files_with_batch.py	31.13% <50.00%> (-0.30%)	⬇️
...ain/scripts/onsite/onsite_create_drs4_time_file.py	38.46% <50.00%> (-0.61%)	⬇️
...n/scripts/onsite/onsite_create_calibration_file.py	25.78% <100.00%> (ø)
...scripts/onsite/onsite_create_drs4_pedestal_file.py	38.46% <100.00%> (ø)
...s/onsite/onsite_create_ffactor_systematics_file.py	32.43% <100.00%> (ø)
lstchain/io/data_management.py	19.29% <0.00%> (+0.33%)	⬆️

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