The blob you show is from COB (chip on board) construction. The chip is not in a separate package. It is installed directly on the board, then the epoxy blob put over it, which substitutes for the chip package. This is a high volume manufacturing technique.
Yes, you can glob epoxy over most electronic things without trouble. About the only issue is heat dissipation. If the part dissipates enough heat, then you have to consider the extra thermal insulation added by the epoxy. Personally I use hot glue for most such things. It doesn't live as long as epoxy, but for prototypes that doesn't matter.
Also consider whether this really matters. Any customer that understands product development will understand that there will be multiple revs of a board, and early revs may have some manual rework. Use hot glue or epoxy to tie things down to make the reworked board mechanically rugged enough, but trying to hide rework sounds silly and probably wouldn't work anyway. A blob of expoxy or hot glue on a board for no good reason looks a lot more stupid than a little rework.