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Not an expert by any stretch - do own a home w/2 flat roof similar as you explain. I have done my own repairs, painted the alligatoriting surface w/rubberized paint etc.

I do know that penetrating a flat roof with what you explain is inviting a whole host of potential problems. And will look really odd. If the roof is intact, not leaking leave it alone. I also have to wonder if what you describe is within code.
We have flat roof above part of kitchen where range is & vented through exterior wall.

Find an alternative option -

Is yours a typical flat roof where there is little or no space between the interior ceiling sheathing and the roof? If so, then the typical reason for using a roof-mounted blower for the range vent (eliminating noise from the kitchen) may not apply to you so much. Most of the time a remote blower like that is located an attic distance away from the kitchen. In yours, you would be gaining less than a foot of "remoteness". So a good quality range hood with an internal blower may be the answer for you.

If you are tied to the external blower, consider checking around the area with roofing companies familiar with your type of roofing, or vendors who install skylights. I would think that the process of installing and sealing a skylight would be very similar to what you're envisioning. I'm not sure I'd DIY this.

see if the ventilator company offers a roof curb. This would be a metal framed box that is designed to seat the unit on it, and seal watertight to the roof.

If you google the roofing system you will find the necessary details but avoid thin paint-like coatings. The silver paint is there to reflect sunlight.

Anything that touches a bitumen (modified asphalt) membrane must be bitumen based; no synthetic rubber or PVC roofing material should be in contact with it.

You should hire a roofer experienced with this kind of membrane roofing. Water damage from roof leaks can easily exceed the expense of the roofer.