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These are separate and complex questions; You should really post them separately if you hope getting some answers
I'll answer to the first one: You do not want to store passwords in Marketo. It is not meant to this. But you would use a Marketo email still and populate it's content from your product through the API, so that the email is sent from Marketo and tracked for opens and clicks. This would be all the more relevant so as you would track login and/or navigation on your product.
As Greg notes, this is complex and it's not a simple answer.
This is something you really have to sit down and work out with the product team. You will have to decide what data will sync between the product and Marketo (not passwords or CC#). Yes, you could have an initial email from the PRoduct, but then pass activation info to Marketo to trigger onboarding nurturing. If you have the correct Status fields, you can certainly tell Trials from Paid, etc.... The only way Marketo knows about emails is if it came from Marketo.
sounds like you are using a webinar or other provide that's not fully integrated with Marketo? Or maybe it is. Telling us the product name would help answer your question. There are third party tools, like Surveymonkey and Vidyard, that can insert data into the Activity Log. I'm sure developers.marketo.com can assist with this sort of thing. But my thought here is to have you research tools that would integrate more natively and for you to create a solution that is simpler than having to custom code. Save the coding for the product integration.
Thanks Greg and Josh. On the special integrations these would be with both launchpoint partners (gotowebinar and webex) and no-launchpoint partners (Cornerstone LMS). The investment has already been made in these tools, so now it's just working to find the best solution.