At some point I learnt this trick and then I forgot it. Today I re-learnt it. And so I’m putting it here so I don’t forget it again.
Basically in a client logo I have there are multiple letters which when turned to outlines have simple rectangles such as L and I (in a sans-serif typeface usually). And these simple rectangles when saved in a PDF often appear to have a thicker weight than letters they sit next to such as P and T (the effect is particularly noticeable at small sizes because proportionately the extra anti-alias stroke is larger when the logo is smaller – when the logo is large, the anti-alias is still probably happening it’s just that it’s such a proportionately small effect that it goes unnoticed).
To avoid this, select the shapes which are appearing thicker and add some points to them, so that the 4 corner nodes of a rectangle get doubled to 8 (so you’ll get an extra node half way between 2 existing nodes). Re-save and update the logo. All should be solved.