Don't be fightened by the fear mongers
The screw threaded through the longeron is exactly how Van's call for the fairings to be installed. Don't worry about it.
Likewise on 6's and others that did not have the luxury of prepunched fuselages, it was necessary to attach the bulkheads to the longerons in the fixture with a rivet, there is no other way to do it. Ideally you try to do it offset from were the row of rivets will go that will attach the skins. When you do attach the skins the rivet at the intersection of the longeron and bulkhead will be close to the first rivet. Leave it along, it is fine. If you have any doubts consult Van's.
If the construction of the airplane is of reasonable quality you will have to have some faith that the correct materials, like the push rod rivets, were used. If you do not you should build your own plane, as that is the only way to insure 100% that the correct material was used. In skydiving I have seen jumpers that have "gear fear", no matter how carefully the gear is taken care of, inspected and packed, they don't trust it. If you can't make the leap to trust your gear (airplane) after reasonable due care, you better take up bowling.
PS: I would be concerned about the soft aluminum fuel line in the engine compartment. The aluminum fuel line should not be used in the engine compartment even if it has a fire sleeve. How is it used?