I can't say I understand exactly what you are asking, but, in general, the hidden assumption of experimentation is that level setting across all factors is similar (e.g., the design space is relatively symmetric). As you suggest, if one factor level setting is much bolder than others, you likely have biased that factor effect and that factor may overwhelm the others. Of course, the challenge is how to set similar levels across completely different scales (e.g., temp is in ºF, time is in seconds, force is in Nm)? The advice I give is to set factors as bold as is reasonably possible across all factors (at least in early experiments). First rank order model effects, then fine tune the level setting. Many engineers are leery of such bold level setting. My hypothesis is they aren't really trying to understand mechanisms, they are trying to pick a winner.
Just a side note, your statement: "That means that something which would have the same effect size in reality would show a signal four times stronger in the experiments." is not necessarily true.
"All models are wrong, some are useful" G.E.P. Box