Thoughts on multiple elbows vs re-routing the whole flue?

Personally, I wouldn't leave a flat run with that many elbows on an atmospheric appliance. I had a 40-gallon Bradford White piped almost the exact same way a few years ago—three elbows to snake around a return drop, dead level. It pulled fine with a smoke pencil in mild weather, but come January when the house was buttoned up and the clothes dryer was running, flue gas was spilling right out of the draft hood. The standard 1/4-inch per foot rise is the absolute bare minimum, and natural draft needs every bit of buoyancy it can get. Stacking two 90s and a 45 in a tight horizontal run creates enough turbulence to stall that weak thermal lift the second a little negative pressure hits the basement. If you can reconfigure the connector to dump one of those 90s and gain even another half-inch of slope, bite the bullet and do it. It's a headache to redo sheet metal on a Saturday, but it beats trusting borderline draft in the dead of winter.

I honestly wouldn't start hacking into your supply ducts or risking clearance-to-combustible issues just to eliminate one bend. People tend to hyper-focus on the connector pipe off the draft hood, but what actually pulls that exhaust is your total vertical chimney height and the basement's air pressure. When I bought my place, my 40-gallon Rheem was tied in with three elbows tucked right under the main trunk line, basically flat over a four-foot span before hitting the common vent. My initial thought was to tear it out, but my chimney has about twenty-two feet of vertical B-vent trough a second story. That vertical column creates so much natural buoyancy that the slight friction loss from those fittings doesn't make a dent once the flue warms up.

The real culprit behind winter spillage isn't an extra elbow; it's mechanical room depressurization. If you seal the house up and run a 400 CFM range hood or a big dryer, flue gas will spill out of a picture-perfect, steeply pitched pipe just as fast. Instead of butchering ductwork, I'd verify your total chimney height and make sure the utility room has a dedicated fresh air intake. If it draws well with other exhaust fans running, you're fine.

What kind of pipe is it right now? If you're running standard single-wall 26-gauge snaplock, you're stuck maintaining 6 inches of clearance to that supply plenum anyway. Swap that connector out for Type B double-wall—grab some 4-inch Amerivent or Selkirk. That drops your required clearance to combustibles down to 1 inch, wich usally gives you enugh headroom to ditch that nasty offset entirely and pitch a straight 45 into the chimney wye.

Remember NFPA 54 tables knock about 10% off your maximum appliance capacity for every additional elbow beyond the first two. Choking down a 40k BTU draft hood with three tight turns on a flat run isn't doing you any favors.

Totally agree you need to re-pipe that run, but check how much straight vertical you have right off the water heater collar before that first elbow hits. alot of guys slap a 90 directly onto the draft hood to duck under low ductwork, but code calls for at least 12 inches of straight vertical rise right off the appliance before your first turn. If you're turning immediately out of the tank on top of having practically zero pitch, you're killing whatever thermal lift you had right out of the gate. Make sure to budget room for that stub when you reconfigure it.

You really need to consult the NFPA 54 vent sizing tables, specifically the capacity reduction rules, because people constantly forget that every 90-degree elbow beyond the initial turn derates the allowable connector capacity by approximately 10 percent (and 5 percent for each 45). If that water heater is a standard 40,000 BTU atmospheric unit on a 3-inch or 4-inch connector with virtually no connector rise, that cumulative equivalent length penalty combined with your borderline slope likely pushes your installation entirely outside of code compliance tables, which mathematically guarantees chronic spillage under adverse pressure regardless of what an ambient smoke test suggests.

If you end up leaving the layout as-is because cutting into that plenum is too much of a pain, just slap a Tjernlund D-3 in-line draft inducer on the pipe. It mounts right into standard connector pipe and mechanically pulls the exhaust so you aren't gambling on weak thermal buoyancy around all those elbows.

I put a Tjernlund on a cramped basement setup a few years back with an almost identical offset and it completely eliminated the spillage issues. Well worth the money over hacking up sheet metal.