fix: consolidate registryConfig application logic

[wraithgar]

It should happen whenever we read a manifest anyways.

Tests were also rewritten to be real.

[npm-robot]

found 1 benchmarks with statistically significant performance regressions

• app-large: clean

timing results

app-large	clean	lock-only	cache-only	cache-only peer-deps	modules-only	no-lock	no-cache	no-modules	no-clean	no-clean audit
npm@8	46.873 ±0.67	27.629 ±0.68	16.032 ±0.07	18.151 ±0.58	2.750 ±0.02	2.762 ±0.02	2.211 ±0.02	10.505 ±0.02	2.204 ±0.01	3.234 ±0.04
#4775	55.642 ±0.55	27.421 ±0.12	25.838 ±13.77	18.341 ±0.37	2.810 ±0.00	2.784 ±0.01	2.213 ±0.01	10.541 ±0.04	2.255 ±0.03	3.290 ±0.14

app-medium	clean	lock-only	cache-only	cache-only peer-deps	modules-only	no-lock	no-cache	no-modules	no-clean	no-clean audit
npm@8	34.219 ±0.93	21.288 ±0.07	11.975 ±0.07	12.737 ±0.13	2.551 ±0.01	2.501 ±0.00	2.226 ±0.00	7.894 ±0.05	2.089 ±0.02	2.894 ±0.10
#4775	36.757 ±0.47	21.450 ±0.00	12.063 ±0.11	12.912 ±0.14	2.528 ±0.02	2.529 ±0.00	2.252 ±0.01	7.867 ±0.05	2.108 ±0.00	2.854 ±0.01