The builder has many choices when building his plane. Many of the parts will be sourced from a kit, others will be sourced from other places like Spruce. Any assembly manual is a suggestion and it is the very nature of experimental that you could bolt the wings on upside down and it would still be legal. There are ACs and other knowledge sources available to mechanics on how to assemble AN fittings. EAB aircraft are built by amateurs and history shows that they are more likely to crash due to mechanical issues. The fact that many builders do a particular task for the first time is probably part of that record.
I think the argument that could be made is in how kits are marketed and the expectations that consumers have. My experience in talking to kit plane sales people at shows who would sell you a kit is, not "I'm selling you an experiment to figure out however you like.", but rather, "I'm selling you a very safe, tested and proven new airplane when built according to our plans." So follow the plans and get a very safe airplane is the expectation.
That's why I wonder how good those plans are in detail. This accident illustrates that little details can be fatal. I really don't know as I have never seen them and I have always heard they are very good in the case of Vans, but this kind of ongoing litigation I believe will put the plans to the test.
A 'loophole' suggests that you can do something illegal just because the letter of the law doesn't allow prosecution due to a narrow legal issue that makes it not apply to a particular case. The FAA recognizes kit manufacturers as integral part of the EAB world and works with them on safety issues if they arise. If the agency that regulates aviation considered the entire kit market a 'loophole', they would have closed it a long time ago. If the IRS finds a tax shelter that they consider a loophole, they fix the regs in the next rulemaking process.
The only 'loophole' is where manufacturers build you the entire plane with their staff and just have the 'builder' come by to sign work log entries. In a couple of weeks with a few hours of his own work, a single 'builder' has now 'built' a turboprop comparable in complexity to a Socata TBM. I am not sure that that is what was intended with the EAB regs.
Well, that's why I put "loophole" in quotes, it's not really so much a true loophole as it is just exploitation. Professional builder assist, "two weeks to taxi" programs, professional builders, all this is not quite what I think the FAA had in mind decades ago when they and the EAA came up the 51% rules. I don't think they envisioned such a large number of serial production, nor did they see planes like the Lancair Evolution as becoming a reality. It was supposed to be about hobbyists learning skills and educating themselves about how airplanes are built, not people acquiring brand new high performance airplanes at a huge discount.
Like you said, if they really didn't like what was going on, they could put the brakes on it. From what I have heard, with accident rates for E/AB being so high, there are those in the FAA that are considering just this. Changing the regs for the 51% rules. However, with GA in this country in decline, I think at this point the FAA is a little bit loath to writing new regs and are more willing to work with the GA community to improve safety without new regs first.