I've never been to Faro, or seen any approach charts for the place. But I am an instrument procedure designer so maybe I can add a few relevant comments.
To take issue with a few points raised back on page 1, the procedure designer works in consultation with ATC for ALL procedures in controlled airspace. The designer does not have to account for aircraft separation as this is ATC's job. That's why we consult with the ATCOs so much.
We can also have approaches to each end of a runway and have the Missed Approach for one going toward the FAF for the approach serving the opposite end of the runway. This is precisely because we consult with ATC and logic dictates that, when weather warrants use of a particular runway, ALL TRAFFIC will be directed to the relevant approach by ATC.
Designers have enough problems ensuring terrain clearance and containment within controlled airspace. We also have to ensure the missed approach has adequate length in which to climb to whatever altitude is needed, at 152FT/NM - the well-known 2.5% gradient. Note that we DON'T CARE about the one-engine inoperative case. That is something between your company SOPs and your regulating authority.
Okay, now, if the 25 MSA is 1400FT, is this just in one sector or all around the navaid? If it's in one sector, is the 10DME holding pattern in that same sector? The reason I ask this is that, if terrain is not at issue, then holding at 3,000 or even 4,000 FT for that matter, is either an ATC or airspace containment issue.
If you don't know the way to interpret the chart, your first line of enquiry is to your company's Safety rep (however you refer to the person in charge of operational safety issues in your organisation). Or your C+T folks, or your Fleet Captain or Chief Pilot.
Finally, yes, as someone else has already stated, Jeppesen really does make the occasional error. Seeking clarification from them is a good move, but that really is best done by your company's Chief Pilot or Fleet Captain, etc. My experience of them is that they DO check their information with the regulating authority and, if they are wrong, they'll fix it PDQ.
Hope this has helped to un-muddy the waters a bit.