Normally, it seems like bridges and tunnels should be mapped with layers instead of level
However, when those bridges/tunnels connect multiple different buildings together, using only layer but not level would cause it being unable to represent that the bridge/tunnel connect those buildings together at certain level.
Is it okay to simply tag those bridges/tunnels with both layer/level in these cases?
If object is on a specific building level it is OK to tag it this way. I for example tagged multilevel train station, with tram tunnel set to proper level value: https://www.openstreetmap.org/way/20196693#map=19/50.06831/19.94769
Wiki is probably meaning that level tag should not be used instead of layer tag,
I agree. layer is useful to know, at a specific point, which way is above and which way is under. level is useful to show all the items that are at the same level in a building. Both may be useful on the same way if a bridge or a tunnel connects two parts of a building.