I can only recommend re-running your math, then. Orders of magnitude differences in energy output will almost certainly yield a different result...
Ideally yes, but here is the math for a TL D 10-ton Wheeled Support vehicle moving speed 4/6, from TechManual (corrected 6th printing):
Engine value: .0075
Movement Factor = 4 + (4x4) = 20
Fuel Cell math:
Engine Weight multiplier (p127): 1.0 (I am ignoring fuel tank mass)
Engine weight: 1.0 * 20 * .0075 * 10 tons = 1.5 tons
Fusion Engine math:
Engine Weight multiplier (p127): 1.0
Engine weight: 1.0 * 20 * .0075 * 10 tons = 1.5 tons
Engine cost math (p280)
Fuel Cell Cost math: 5000 * 1.5 * 1.4 = 10,500
Fusion Engine Cost math: 5000 * 1.5 * 2 = 15,000
(Final Structural Cost and Final Unit Cost formula ignored as it would be identical for both; 1.0 & 1.05)
The extra weight for a Fuel Cell is from the spare tankage needed to travel distances, while the Fusion plant doesn't need to worry about that detail. Beyond that they both mass the same and the Fuel Cell is 30% cheaper.