[Transform] wait for checkpoint does not refresh the dest index

[hendrikmuhs]

When using wait_for_checkpoint the destination index should be refreshed, so that documents are searchable after _stop/wait_for_checkpoint=true returns

found in #51033

[elasticmachine]

Pinging @elastic/ml-core (:ml/Transform)

[hendrikmuhs]

This has been fixed as part of #67832, however this issue is still mentioned in some places in code with workarounds. These should be removed to finally close this issue.