I’ve spoken with the relevant engineer and been told that those recommendations (3.5Nm for the penetrators, 0.6Nm for the end-cap bolts) should be fine.
On this front,
It’s a face seal o-ring, so too much compression is impossible
You’d break the screws as the aluminium bottoms out
My understanding is that o-ring over-compression is more of a design consideration than an installation one - even more so in face-seal cases, where the components being connected are meant to be solidly pressed against each other, rather than having a gap.
When installing it’s important to ensure the o-rings and surfaces are clean and correctly lubricated, and in the right position (it shouldn’t pinch on a corner - gradually tightening the bolts in a star pattern can help avoid this). If a leak occurs it’s very likely that it’s from some dust or hair or a small cut or gouge in the o-ring that has compromised the seal, rather than an issue with the amount of compression (which has been designed for).
If it’s any further peace of mind, there’s a blog post here which covers o-ring squeeze ratios, and recommends 25% squeeze for static applications of NBR70 o-ring seals. Our face o-ring is listed as AS568 size 154, which according to here has a cross-sectional diameter (CS) of 2.62mm \pm0.08 mm. In the provided CAD model our 4" Flange has a gland depth of 2.06mm. That gives
which is very close to the recommended 25%, and also fits well within the ‘rule of thumb’ presented here for 10-40% compression of static seals.