The filter arrangement is not good installation practice, the use of the additional standard filter prior to the Aprilaire filter is done to “pre filter” the dirt to keep from changing the more expensive filter as often. The air flow restriction of the Aprilaire when new is very high, when dirty the system is close to failure from low air flow, by adding the “pre” filter were compounding the restriction and reducing the air flow even more and not adding any measurable life to the Aprilaire filter which is up to 97% efficient. This was mot likely a sales gimmick playing on the home owner request or just an idiot HVAC guy.
In situations where the high performance filter here the Aprilaire (one on the left) was not present and you only had the standard filter in the slot of the return air drop no need to “cap” over the filter, code normally will not dictate this and the risk of recalculating combustion air in to the house air is almost non existent, and “using up” the make up air or combustion air by drawing through the area around the filter is also almost non existent and most codes will not address this. Caps over the filter are higher end sheet metal work by better HVAC companies that charge more, while it looks better lack of a cap is not wrong under most older codes, although this is changing as more codes include provisions from the energy conservation act requiring tighter ducts.
The furnace you have pictured here by the look of the circuit board is a 80% efficient furnace, and when installed on masonry chimney with out a metal flue liner will cause mortar break down but may not have been required under code and installation guidelines depending on what year it was installed.
Prior to the 80’s we had furnaces in the efficiency range of 60% and lower, the amount of heat sent up the chimney was sufficient to warm the brick and provide proper venting.
In the early 80’s the 78% , 80% & 82% efficient furnaces were introduced. The amount of heat removed from combustion was greater resulting in cooler flue gases, but in the beginning no one knew this would be an issue. But after about 5 yrs home owners were having chimney failure, heat exchanger failure, carbon monoxide and carbon dioxide was leaking into the home through the mortar of the chimney as it broke down. Result many law suits.
The reason then and today that the chimneys break down is that the gases cool as they rise up the chimney, they cool and condense on the inner chimney with or with out a clay liner, the acidic level of the gas breaks down the mortor and rusts the heat exchanger. So liners became recommend under certain conditions. The liner protected the chimney, and the smaller surface area of the liner would heat properly to allow complete venting to the roof.
In the late 80’s into the 90”s the manufactures standardized on the 80% efficient level and recommend a flue liner only on chimneys on out side walls with out a hot water heater, again after several years more law suits.
Today liners are recommend by most manufactures for all installations of 80% furnaces on masonry chimneys
80% furnaces have a power venter but this does not push the flue gases up the chimney, this is basically still done by convection of hot air rising, the venter only pulls the gases through the heat exchanger.
Furnaces in the 90% range do not use liners nor do they vent by convection of hot air rising, they use only PVC pipe and the flue gases are pushed out side by the power venter motor. They can not be vented by convection because the average temp of the flue gas is around 90 degrees, far too cool for any type of chimney or metal vent. The PVC can be vented vertical or horizontal with each manufacture having a limit on the distance the PVC can be ran and if it is a one or two pipe system.