Please see replies

- Is the flyer still able to collect individual membership miles if the flight has been redeemed from company plus miles?

Yes. In order to claim the points in Company Plus you have to enter (or upload) the ticket information.. (Passenger name, start/end airports for first segment, class, flight number etc). Alternatively you can upload information about the credit cards used.

- My department mostly (not always) uses special tickets associated with the work we do, to get these we have to go through agents. Can we still claim the company plus miles or are they eaten up by the agent? You can still claim them as you have to upload them to the Company Plus system under your account.

- Any other suggestions, advice or experience with such proposals (particularly why anyone would object in the long/short run)?
No one should object in truth as it is invisible to the actual passengers; I think that even check-in agents don't know you have put in a claim for points.