Jared Caron
Nursing leader; GTD enthusiast
I use a similar approach in todoist, and I'm also microsoft based at work. If an email is critical to the task I will leave breadcrumbs in my notes so I can find it. If my filing system is good, there's no friction to finding it later.
I know others are recommending automation, but I would suggest caution here. Part of the value of manually handling the processing/clarify step is intentionality. Yes, it can take longer but it's you making the decision, and your brain can be much more nuanced and intelligent than any rule you can cook up (especially in the new outlook where rules are basically pointless). In my world there's often a lot of interpersonal, political, and situational context in emails and trying to be too rigid with automation would undermine my opportunity to assess how best to handle them. Sometimes it's more about effectiveness than efficiency.
As for your original question about flagged emails, here's my take:
I have found over almost 10 years of GTD that the allure of linking things together inside your tools is kind of a mirage. Looks great from a distance but up close it evaporates. Through practice I've learned to trust my mind to manage the connections and relationships. You may be surprised how well you can do this when the job of "remembering" the actions and projects is externalized in your system; your brain is way better at this than any app. I have found that simply having the right lists, a solid reference and project support system, and really leaning into complete capture are all you need. More often I've foudn that trying to create the perfect linking between projects, next actions, reference, project support, and communications simply leaves my spending more time working on my system than working with my system.
All that said - much of this is idiosyncratic and individual. So do what works for you. There are no rules, only principles and best practices.