Prevent the default value from being used when values were already passed

[kinow]

Closes #1632

I think this should fix the issue reported, but not sure if there are other cases (file/directory) that would also require a similar fix.

[codecov]

Codecov Report

Merging #1675 (14ad829) into main (202b682) will decrease coverage by 0.03%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main    #1675      +/-   ##
==========================================
- Coverage   66.86%   66.83%   -0.04%     
==========================================
  Files          93       93              
  Lines       16622    16648      +26     
  Branches     4414     4420       +6     
==========================================
+ Hits        11114    11126      +12     
- Misses       4366     4380      +14     
  Partials     1142     1142              

Impacted Files	Coverage Δ
cwltool/argparser.py	94.82% <100.00%> (+0.28%)	⬆️
cwltool/cwltool/argparser.py	72.11% <0.00%> (-2.68%)	⬇️
cwltool/cwltool/job.py	61.85% <0.00%> (-0.80%)	⬇️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 202b682...14ad829. Read the comment docs.