1) "Foundations of Physics" is closer to a philosophy journal than a physics journal. It's full of fascinating stuff, but it's far more speculative than any other legitimate journal. When libraries were cutting budgets in the '80's and '90's it was generally the first to go.
2) When highly theoretical phenomena are talked about in engineering terms, the odds of confirmation bias are huge. Who wouldn't want a reactionless-ish thruster?
3) Measuring transient forces of the kind being applied here is extremely hard, and the number of confounding factors is extremely large. The article mentions a mu-metal shield, which will screen some of the Earth's magnetic field from the apparatus but which is useless for screening transient magnetic fields, which get generated by transient electric fields thanks to the magic of Maxwell. Ampere's law tells us CurlB = mu_0epsilon_0dE/dt. So the possibility of residual electro-magnetic forces is non-trivial to say the least, particularly in a room full of conductors and time-varying EM-fields (from the wiring, the pump, etc).
Putting the whole apparatus in a Faraday cage would help, but the history of measuring small (and transient) forces in physics in the past couple of decades (the fifth force mess, Joe Weber's coherent neutrino scattering work) argues that we take these experimental measurements with a large grain of salt, unless they can be shown to be in precise numerical agreement with the theory's predictions over an order of magnitude variation in power input and rate of variation.
The theory may not be wrong, but it needs a lot more experimental investigation and likely theoretical examination as well. Theorists tend not to spend a lot of time critiquing things that look really likely to be wrong, because proving something that everyone thinks is probably wrong, wrong can be incredibly time-consuming and utterly unrewarding. So the lack of theoretical disproof is not very compelling. So far as I know Joe Weber's coherent scattering theory was never dis-proven in publication, either: it was mostly dismissed by informal but compelling arguments at conferences (the best one was simply that there was nothing special about neutrinos in Weber's theory, so if what he said was correct single crystals would coherently scatter x-rays in exactly the same way, which would have shown up as an anomalous low-energy contribution to EM cross-sections that would have been an obvious problem for decades if anyone had observed it.)