One possible problem with a "centreline twin" would be the LACK of response due to engine failure. While a conventional twin goes asymmetric on engine-out, giving a pretty obvious cue to the crew, a "centreline twin" would do no such thing. There would be concerns, i am sure, over the ability of a crew to promptly recognize and respond to engine failure. The concern would not be their inability to maintain centreline - that would be easy - but rather the risk of taking longer to recognize and reject a TO. I would not be surprised to find the current "2 second rule" be extended to some longer time period, and/or some very specific additional warning/monitoring be required.
The regulations do provide for some of this:
§25.107 Takeoff speeds.
(a) V1 must be established in relation to VEF as follows:
(1) VEF is the calibrated airspeed at which the critical engine is assumed to fail. VEF must be selected by the applicant, but may not be less than VMCG determined under §25.149(e).
(2) V1, in terms of calibrated airspeed, is selected by the applicant; however, V1 may not be less than VEF plus the speed gained with critical engine inoperative during the time interval between the instant at which the critical engine is failed, and the instant at which the pilot recognizes and reacts to the engine failure, as indicated by the pilot's initiation of the first action (e.g., applying brakes, reducing thrust, deploying speed brakes) to stop the airplane during accelerate-stop tests.
(1) will likely be trivial, but the recognition time in (2) will then come into the fore.