So you can't just have jump ships hold the door open for your fleet and stay on the other side, right? They have to jump with the fleet?
You can do this. I can't remember if they can hold the door open, but a jump ship does not have to jump with the fleet unless you are doing a squadron jump, so you can send in the fleet, then send the jump ship through later to jump them all back (if even needed, I can't remember for sure but I think a jump ship can jump ships from the other side too?).
How much of a bad idea would it be to just not give them engine and have them towed into position instead? I can't really give my tenders reasonable speed and range anyways while keeping them at a reasonable tonnage, so screw it, right?
This would work especially well as part of a tractor-trailer strategy - where you use a lot of tugs to move things around, and build a variety of oversized modules for freight, colonists, etc. as engineless space stations. Though I don't know if jump drives can be put on a space station, probably not, but the same principle applies. This would mean you always have tugs to move your jump tenders where you need them.
The only catch is that you need to have two fleets, the military fleet and a separate fleet with a second commercial jump pod to jump the commercial-engined ships i.e. tugs.