Because speakers work in a room and every room is different. Headphones work on heads and ears that are much more similar between different people.
Your whole problem makes limited sense to me, based on the description. Surely, smaller speakers on a desk can have more pronounced bass than larger ones elsewhere, depending on the room response. Which one is more accurate is another matter.
When you compare the same speakers with different apps, and some apps produce more bass than Roon, then either the other apps amplify it with some DSP or Roon deemphasizes it with DSP. Doesn’t seem like there are other possibilities.
Roon provides a signal path graphic telling you what happens in Roon, so please post this as a baseline:
Other than that, check if other apps (or the speakers when used with other apps) enable a setting for DSP you aren’t aware of.
If the signal in Roon is flat and you think the bass isn’t enough then the problem isn’t Roon but more likely the way your speakers work in the room. (Or it’s possible that it’s just accurate and you are used to empathized bass. Not saying that’s the case but it is possible). Close to the wall doesn’t necessarily always lead to pronounced bass. It causes a comb filter effect that can lead to low energy precisely in the listening position.
I’d recommend measuring the room and creating a convolution filter that you can load into Roon for room correction. As you seem to have an iPhone, HouseCurve is a cheap and quick way to get this done:
There is a thread on the forum about it:
However, note that no room correction can fill in bass nulls because the problem with these is that the room acoustics suck out the energy at specific frequencies at specific locations in the room, and trying to fill these nulls leads to amp overload. The only solution for that is playing with speaker placement and listening position (but the good thing is that a few centimeters can make big differences).
I’d first try to get the physical speaker placement and listening position as good as possible,
then make final corrections with DSP like with HouseCurve