This is not supported in the exporter and we have no plans to add it. Most exporters use a different approach, which we recommend for exporters in general.
Deploy the expory as a sidecar alongside the MySQL instance. In Kubernetes, this means an additional container in the MySQL pod. This solves your problem by making each MySQL+exporter pod its own scrape target with its own instance label.
For most exporters, the way to think about them is not as a separate service that somehow interacts with what it is translating for (in this case, MySQL). Rather see the exporter as an out-of-process plugin, paired 1:1 with each MySQL process. For the purposes of monitoring, they are one unit, and when looking at metrics and alerts you don't need to worry whether a piece of software supports Prometheus natively or through an exporter.
I hope this helps!