Use `ExtendOverwriteDefault` for all multi-value options #3153

Job	Run time
mypy	51s
pathogen-repo-ci (dengue)	2m 51s
check-docs	38s
pathogen-repo-ci (lassa)	7m 26s
pathogen-repo-ci-v0 (avian-flu)	1m 3s
pathogen-repo-ci (measles)	1m 19s
pathogen-repo-ci-v0 (ebola)	53s
pyright	16s
pathogen-repo-ci-v0 (mumps)	55s
pathogen-repo-ci (mpox)	1m 21s
pathogen-repo-ci-v0 (ncov)	58s
pathogen-repo-ci (oropouche)	1m 17s
test (python=3.9 biopython=1.80)	1m 2s
pathogen-repo-ci-v0 (rsv)	8m 58s
test (python=3.9 biopython=1.82)	1m 7s
pathogen-repo-ci (rabies)	2m 16s
pathogen-repo-ci-v0 (seasonal-flu)	1m 9s
test (python=3.9 biopython=latest)	1m 10s
pathogen-repo-ci-v0 (tb)	1m 16s
pathogen-repo-ci (seasonal-cov)	1m 59s
test (python=3.10 biopython=1.80)	1m 3s
pathogen-repo-ci (wnv)	1m 1s
test (python=3.10 biopython=1.82)	1m 7s
pathogen-repo-ci (yellow-fever)	4m 13s
test (python=3.10 biopython=latest)	57s
pathogen-repo-ci (zika)	1m 0s
test (python=3.11 biopython=1.80)	55s
test (python=3.11 biopython=1.82)	1m 9s
test (python=3.11 biopython=latest)	1m 2s
test (python=3.12 biopython=1.82)	1m 12s
test (python=3.12 biopython=latest)	1m 12s
build-docs / build	2m 36s
release	0s
codecov	0s
rebuild-docker-image	0s
	56m 12s

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