Having parallel cells like this is not so peculiar when you think about it. A single cell is a rolled up sandwich of electrodes and insulator. In effect, the whole cell is "in parallel" throughout. If a D cell were made, it would just consist if a much fatter roll consisting of a longer strip of electrodes. What we have in the Eneloop D cell is the same long strip cut up into three pieces and made into three thinner rolls. Electrically it is much the same as one fat roll.
Charging in parallel for NiMH cells can be acceptable, as others have said, if all the cells are identical, from the same batch, connected with equivalent circuit paths, and treated the same way. Most importantly, all the cells should be in good thermal contact so they maintain an even temperature.
Problems can happen with parallel charging if the cells are allowed to attain different temperatures. In that case any cell that gets warmer than the others will drop in resistance and steal extra current from the charger, making it warmer still. The positive feedback of higher current and increasing temperature can lead to thermal runaway and cell damage. This is the main reason for recommending against the charging of NiMH cells in parallel.