I would doubt very much from a 'chemistry' point of view that the UV agents (typically micronized and nano-sized ferrous oxide particles) would migrate from a gelled substrate 'up' and into a freshly applied layer of varnish thus diluting the 'begun to harden' and partly 'dried' layer.
Flagship is an oil based varnish and thus is 'botanic' based and therefore not so easily controlled as to lot to lot consistency due the variability of grown agricultural/botanic components in such a mixture as an oil based varnish such as 'Flagship'. Such variability could indeed be the cause of any particular problem, but really not a migration of inorganic micronized ferrous oxide. the ferrous only to provide UV protection of the surface wood cells.
Another consideration, if not a thinner/mixture issue (viscosity), and if using 'oil based' varnishes is the variability of absorbtion into the surface of the wood ... and the reason that 'the ancients' always used a 'ground coat' or sealer when applying varnish to supreme quality musical instruments and supreme quality woodwork to totally control the absorption rates so to get dead flat upper surfaces ( aka: orange peel, which could be a relative absorption problem .... or a lay down that is simply applied 'too thick', a common application error with 'varnish' that greatly prolongs the 'dry' time).
So too, the modern EPA constraints which limit VOCs, etc. are probably a contributory factor ... and the probable reason for many 'fine' and 'museum grade' finishers to now make their own varnishes. My dad, as a very profitable hobby, did such 'ultra' and museum-grade finish work and usually made up his own varnish and 'ground coats' simply to maintain uniformity and consistency.
Silicone contamination will usually shows up as 'birds eyes', not orange peel.
Heres a pic of ferrous oxide loaded totally synthetic 'varnish', actually a catalyzed urethane/acrylic, a modern co-polymer 'varnish' (Honey Teak) that has been heavily flat sanded and heavily polished (and hand rubbed - w/ rottenstone) that is over 12 years old (just an occasional maintenance 'top coat' with clear) using essentially the very same UV filters as now found in 'outdoor' oil and urethane based 'varnish' .... but all the UV filters are in the initial 'base coats' and has many 'clear' coats over that.
I have zero thought that the lower UV stabilizers of, oh 14-20 layers of varnish somehow move from cured layers upward to wet. I do not intend to convey that. Thanks for the opportunity to clarify.
I do have total belief that within the wet layer such migration takes place.... Now follow...
In a high-coat high-build finish, (up to and beyond 20 coats) we sand everything off but the low spots. We are grain filling. If the hypotheses I propose is factual, and the recommended sanding between some random number of coats as recommended by the manufacturer is followed, the only place these UV inhibitors will remain is down in the grain or in the low spots of the finish.
Following this logic, the folks who religiously sand between every coat have the least UV protection, (or the crumminess-looking filler stain layer on the planet). For those like myself who sand after every 4, the odds are better, except for the fact that 4-varnishes are heavy sanders. Bottom-line, and again if hypotheses hold true, even though you are applying UV varnish, your sanding is reducing its UV stability to that of straight epoxy, (zero over much of your varnished surface).
So....
Tying your post to mine, I say first I agree completely. Little microscopic rust flakes don't move from dried varnish to wet. They live in the wet layer, only to float to the surface to be rubbed away.
Then I counter that your cited example would require less work if it were built, flattened, polished, then very lightly abraded and finally coated with a UV varnish. THEN left as-is.
It is this exact process I speak of. Varnish/sand/repeat as many times as necessary to achieve your desired flat finish. For some it is 3 coats. For others it is epoxy followed by 30 coats. Sand a last time, lay a coat on, and then don't touch it with anything harsher than water and a terry cloth towel until the next time, (my experience is 3-8 years) you decide to varnish.
It is this finish protocol that allows a uniform layer of a final topcoat to cover and seal every prior coat that has been applied, without regard to how those prior coats were removed. If 15 coats gets you a block-flat sanding base with no low spots, coat 16 will go on and lay down flat as if applied to sheet glass. And as such you can leave it completely alone, with all chemical protection intact.
Bottom - line: my advice is this. If you want to minimize your maintenance coats, don't sand the final varnish coat on top. Leave your sunscreen on!