The smell coming through the HVAC system

The easiest and most cost effective way of dealing with it is to paint over it with something like drylok. You can't really do anything about the smell itself other than removing the epoxy but you can put up a good barrier.

It depends on the home, and the system. Neither of which you've provided much information.

Older homes are usually drafty enough to provide adequate combustion air, so dedicated intake are not required. Modern homes tend to be sealed up much tighter, and often require air intakes.

Sometimes systems are installed in a utility closet, or other space where makeup air can't be drawn from surrounding areas in the home. In these cases, an air intake will also be used.

Some modern furnaces actually draw air from outside, directly into the unit. This reduces the amount of cold dry air that is pulled into the home.

If you're simply concerned about the quality of the air entering the home, it's possible that you could install a filter on the intake. Though you'll have to make sure you don't restrict the amount of air being drawn in.

If you don't have carbon monoxide detectors in the home, you'll want to install some.