There is a messy trick to work around this- you can fill up a workshop (for your legendary dwarf) with dummy jobs on suspend. Say you want 20 orders of blocks made, but still want your legendary mason to churn out masterwork coffers to outfit the new migrant wave. What you do is leave the scud labor workshops empty. Your legendary mason workshop has your "Construct rock Coffer" set to repeat, then has 9 other "dummy" (tables, thrones, doors... anything but blocks). Or you could just fill his workshop up entirely with suspended jobs to keep it on standby. Just make sure to set a maximum skill level (talented maybe?) on your scud labor workshops.
When set up right, your legendary mason workshop will be passed over by the manager (since the workshop is full) and the scud workshops will get filled up with the job. However, if you have less workshop-job space than job's queued up, when you start working out of your legendary workshop order jobs might start popping up.
Its more micromanagement, but its the best workaround you can do other than simply not using the manager. I do agree with you in that the manager should respect workshops. Personally, I'd like to see a key to either assign the jobs through workshops, or be able to assign a profile to the job order (like you can a workshop). So when you order "30 rock blocks" form the manager, you can adjust the profile to only assign to workshops that have certain skill levels enabled. So your "construct rock blocks 30: dabbling skill min/talented skill max"