I've had diesel in a pair or those Rotopax 4 gallon containers mounted up under there since Feb and I have not vented it once. Been from near freezing to over 100 degrees and no leaks or any issues.
And in regards to the "structural integrity" issue of removing the tire winch, You need to look for your yourself. On my 2005, it is just that, a simple little tire winch with 2 bolts holding it in place. It provides ZERO structural enhancement to the van. Perhaps other years are different or maybe you are talking about cutting out more stuff under there but I made the Rotopax mount possible by simply removing the spare tire winch and drilling a few holes to the existing bracketry that is under there.
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Glenn P.
2005 Quigley E350
6.0L Diesel
If not already linked:
Post #8 covers everything about removing the OEM spare tire X-brace. The frame cross member forward of the spare tire space should not be removed.