Currently the TLS certificates for jaeger as well as the ingress configuration is deployed using the jaeger chart config value extraObjects (in deployment-charts/helmfile.d/aux-k8s-services/jaeger/values.yaml).
While that works, I would consider this a bit of a hack as the objects created there are not actually part of the chart and lack quite some dynamic templating. It won't be possible for example to install a second jaeger release (for testing or whatever) without manually fixing those extraObjects for the new release and there is also quite some duplication.
Most of that can probably be worked around by extending templating in extraObjects but that is very painful as special quoting rules apply for that (yaml objects being interpreted as strings treated as go templates which will then be converted to yaml objects...).
Personally I would extend the jaeger chart with maybe a wmf-additions.tpl file or something where all those extraObjects go into. That should not effect the backporting of upstream changes much and has the benefit of being versioned (by the chart version) as well as having the full templating system available.