Does cron.yaml support conditions?
As far as I know, that isn't possible.
The Cron.yaml page is only made for defining the jobs, not to code.
I'd recommend putting your logic inside of the job that you're calling, as you mentioned.
Hope this helps.
Is it possible to have conditions (if ... else ...) in GAE cron.yaml?
For ex., to have something like 
if app_identity.get_application_id() == 'my-appid' then run the job.
Understand, that probably the same result I can have by implementing it in the job handler. Just interesting if it could be done within cron.yaml.