In all boats there are what are termed dead spaces .... enclosed areas that are not actually used as lockers etc. You may be able to convert a seemingly closed space into a new small locker to fit the unit ... keeping it away from damp etc.
Another area is most under-bunk lockers have space that could be sectioned off with a small bulkhead ....
It takes a bit of ingenuity - but I'm sure that a small space can be found that is unused, suitable for a little conversion work ... much better than a cockpit locker ....
Yeap originally was going to put it near batteries under bunk in aft cabin. Only concern was whether it would get enough air not to overheat. But it would be the easiest (from point of view of running leads to the batteries) and tidiest place.
It's easy to improve ventilation with a tiny computer-type fan. If you get a mains voltage fan and wire it in to the charger's input, it'll only run when the charger's on. Maplin do some suitable fans, see here for an example.
I have a Merlin Charger, forget model but does boost, normal & float charge, fitted under aft cabin berth, on side of battery box. Large heat sink (standard) overcomes heat problems for charger, haven't had any problems in 3 years anyway, with added advantage of background heating for berth, not so good in summer but then sleep in forepeak berths.
The after berth might be a bad choice - check first to see if you get condensation under it, or dampness in the bilge below due to the rudder gland. Any locker that is formed by a bilge section is potentially dodgy as warm, moist air condenses on cold fibreglass, cooled by the sea. Great place for keeping your beers, though!