Is it safe to put the stem directly on top of the "dust / top cap" of the headset without any spacers?
This is true, I have better flexibility now that's why I want to shuffle the spacers around.make sure you pay attention to fit more than looks, IMHO.
A properly fitted bike should have a proporcional long stem with no spacers under ( for a 56cm bike a 120mm stem, for a 54cm a 110mm for example )
If you need spacers there is for one of two reasons
1. the frame is too small for you. in that case your stem should be also long ( 130 and plus )
2. you haven't trained your back ( and/or reduced your gut ) to have enough flexibility
This isn't theoretical, it is incredibly practical. I don't know what sort of fit articles you could possibly be reading: Between sizes 48 and 62 you'd need to have 8 different stem lengths - do you really think all short people are riding 80mm stems and all tall people use 150s? That's patently absurd. Stems come in increments smaller than top tube increments because people's backs, arms, legs and everything else come in increments a lot smaller than that.Well, my post comes from my own experience fitting and riding many frame sizes and stem lengths and heights combinations and at the same time going through a process of training myself to have a better position on the bike.
Add to that my activity of hobby bike builder where I had built and sold some 40 racing bikes and helped many of the buyers to get an optimal fit and improve their own position on the bike.
I had found that ( for me as an example ) the best fit on a bike for all positions, that includes, a cruising on the bends, a flat back or descending on the hooks, a climbing off the saddle on the hoods and sprinting on the drops is with a 56cm (55cc) frame with a 120mm stem, that gives a 55cm saddle handlebars and 55cm front hub handlebars setup.
On a Colnago C50 or equivalent racing bike the setup is exactly with a -6 degree stem without spacers.
I can get the same setup on a 54cm frame with 130mm stem but I am then too forward, or the same with a 58cm 110 stem -17 but I am too on the rear, I had experimented with a 57cm, 59cm, 55cm and different stem lengths and heights combinations but even if one position could be right the others were slightly off.
The 56cm/120mm or equivalent 52s/120mm is the optimal.
Proportionally a smaller frame would need a shorter stem and viceversa, as I have read on some fitting articles.
And well there is too the rider's fitness level to adopt himself the best position ( that comes with training ) instead of the reverse approach that is to adapt the bike to the lower level of fitness of the rider with comfort geometries or stacks of spacers and short stems.
HTH, I am just giving my own experience and findings here, not a theoretical dissertation on fitting or frame design or market trends.