Pumps are attached to stools or seatings on the tank top - welded these days but probably riveted in 1912. The only part of any machinery that pierces it are the holding down bolts for the main engine(s) and thrust blocks. That's current practice in ships today, so would have been the same then.
I sailed on a 110,000dwt ore carrier where most of the holding down bolts were slack and many were broken. To rectify this meant removing the broken ones (the bolt end had fallen into the double bottom (DB) in way of the cofferdam round the engine (ie it's not a water or oil space, it's supposed to be dry, as there are grommets on the bolts to stop bilge water running into the cofferdam. As so many bolts were broken though, we pumped the bilges by pumping out the cofferdam as the water was running through the slack and broken bolts...
The double bottom on that ship was the standard 3m, with lightening holes to allow passage round the engine bolts, which were 1m+ above your head if you were 1.82 like I was (it was a job for the tallest engineer you had). To replace a bolt you took the new ones into the cofferdam with you (they were heavy, believe me), with a grommet fitted round the bolt head. Standing on the lightening holes meant your feet were around a metre or more above the bottom plating, so astride two lightening holes with the bolt in your arms, you had to proffer it up to the hole - which you could see because your oppo above had a torch shining down it... Once into the hole, your oppo fitted a flat washer and then the nut, as you were sweating like a piglet in a confined space with your arms outstretched holding the thing in place (you made sure the threads were clear and the nut would spin on before you disappeared into the rather claustrophobic space). With some 160 bolts to hold down the engine and with at least 20-30 broken, this was an arduous task undertaken by the 4th engineer (up top) and the 3rd Engineer (me) in the cofferdam.
On completion we went round and flogged up all the loose bolts.
Attached is a sketch of the arrangement where I've marked the cofferdam. You can see where the holding down bolts project into it through the chocking arrangements.