keys of size 4096 cause noticeable performance issues, so they are normally used only for certificates that need to last for a long time (like CA keys that need to last for 20 years). FIPS for example still only allows 2k and 3k keys.
Our certificates are relatively short lived so we should use a longer key only for the CA.
In general configurability is a good thing because different customers may need different security/performance/compatibility tradeoffs.