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Imagine a waste heat driven pressure swing adsorption device is used to treat automobile exhaust gas. Further it aggressively scrubs nitrate, sulphate and CO2 emissions. Note: tanks and filters would require changing with each refueling.
Would there be any potential environmental downside to adopting the use of such a machine if it can scrub CO2 much faster than the vehicle produces it?
There are no potential environment downsides from scrubbing CO2 faster than it can be produced. With the exception of the material residue from the scrubbing process itself, but without any further details of the scrubbing mechanism itself and what chemicals this might involve makes this possible problem purely conjectural.
More CO2 is produced by industry and power stations than by car engines, so the net reduction in CO2 emissions will be not necessarily minimal but somewhat less significant than usually realized. However, if your proposed scrubber could work with aircraft engines the CO2 emissions reduction would be reasonably significant. Better if it can be used for industry and power stations.
In summary, no potential environmental hazards are likely.
Here is your biggest environmental problem:
Note: tanks and filters would require changing with each refueling.
You're offsetting the CO2 from the vehicle into a separate manufacturing and waste cycle. You have not reduced pollution, but rather increased and outsourced it.
CO2 sequesterization at the power plant level takes about 10% of hte net energy to get about 70% of the CO2. In this case the CO2 is pumped into deep (2000m) wells.
To get this to happen at a transport level, you need to convert CO2 into a liquid or solid. This isn't unreasonable: We store CO2 in fire extinguishers all the time. So the gas station would just pump out the CO2 when you pump in the gasoline. This would be roughly comparable to the tech used for propane fueling.
Someone who knows more chemistry than I do can speak to the irreducible energy cost of separating the CO2 from the exhaust.
The other part, the nitrates, are already done with diesel engines. You add urea to the exhaust which breaks down the NOx. Sulfates are mostly an issue with what is in the fuel. Low sulfur fuel is now mandated by law. I don't think it's currently an issue in North America or Europe.
This however may be the hard way.
A: Convert fossil fuel to electricity, with CO2 scrubbing. B: Charge electric vehicles.
This eliminates the problem of carrying around a huge apparatus on each vehicle that is only used part of the time.
At present coal fired power generation is at best something like 50% efficient, with older plants being in the mid 30's. There is a possibility for solid carbon fuel cells. This is a non-thermodynamic process potentially 80% efficient. CO2 is produces as a pure gas make sequesterization much easier. To make this work, however you need very pure carbon. Not quite ready for prime time.
https://publications.csiro.au/rpr/download?pid=csiro:EP104697&dsid=DS9
