I found one way round this by hardcoding labels in the receiver configuration, however this seems to overwrite the jiralert label ALERT(key=value) which appears to be used to prevent duplicate tickets opening.

fields:
  labels: ["CFT"]

Further to my last post, I managed to overcome the duplicate tickets issue using the following configuration. This works though might seem a bit of a hack.

config/jiralert.yml

fields:
  labels: ["CFT", '{{ template "sm.labels" . }}']

config/jiralert.tmpl
{{ define "sm.labels" }}ALERT{alertname="{{ .GroupLabels.SortedPairs.Values | join "," }}"}{{ end }}

I now have two labels on the jira ticket:
ALERT{alertname="TestAlert"} CFT

Wow, impressive problem solving skills. (o:

Yeah, the labels should be cumulative, but I guess any label you set via fields.labels will overwrite the ALERT label used by JIRAlert to identify which alert this is.

Will need some code tweaks for special handling of custom labels added via fields.labels. Might also need to check if any other fields need similar special handling (although most of them are single-valued rather than lists, so overriding is likely the expected outcome there, even though it wouldn't make much sense).