Okay, this is a rare question about baseball cards that I feel qualified to answer on this forum!
To answer your query, 1952boyntoncollector, in my experience, modern collectors prefer on card autos to a large degree. I know I do. Why? There are numerous reasons. The first, as you mentioned, is that with an on card auto, there's the feeling that the player actually held the card in his hand, and signed it. There is a personal connection that, for me, is much more appealing. Does it add monetary value to the card? Not necessarily. But I would much rather have a card that was held by the player than a card that just had a sticker auto slapped on at a later date. Personally, if an older player were to mass sign a sheet of sticker autos, what's to stop the card manufacturer from making "new" autographed cards posthumously? This doesn't pertain to the young guys playing now (for the most part), but companies like Topps, Panini (Donruss), etc have product lines where the greats of the game do sign. Think of Topps Archives. New cards are printed in the style of releases from the 1950s, 60s, etc, and then signed by the greats of the game. Those cards are designated either with a gold foil emblem, or "Topps Certified autograph", etc.
Think of this. Some day, hopefully years from now, Willie Mays is going to go to the great diamond in the sky. Would you rather buy a card that he held, and signed, or one made after he died, with a sticker he signed four years ago slapped on? Forget the monetary value. From a pure aesthetics standpoint, on card signatures are always more appealing (at least, to me). These sticker autos are peeled off, and then slapped on their cards. Sometimes they are not straight (though it's less of an issue now). And even worse, because there is a finite amount of space to the sticker itself, players with more embellished signatures will actually see part of their autograph cut off. And if a card is graded, that will lower the auto grade by a full point.
That impacts the resale value.
When you consider what these "premium" boxes cost now, I won't even buy a box if the autos are going to be stickered. I haven't bought a box in a year or so, but I only buy Bowman Chrome baseball card boxes, as all the autos are on card (with one exception, the USA Olympic cards. Those are stickers).
As to some of the nice cards with on card autos you inquired about...here are a couple of mine. Sorry about the variance in size. I will be buying a new scanner soon, and I'll re-scan some of these.
2009 Bowman Chrome Mike Trout auto.
2011 Bowman Chrome Bryce Harper auto
2012 Bowman Chrome Jose Fernandez auto
Compare these two cards, and tell me which you like better:
I like the design of both cards (the Museum card is much thicker), but the gauche sticker on the Justin Upton rookie knocks the card down a peg, in my opinion. The Museum card, with the clean, on card auto, is just beautiful to behold.