By doing this type of install your limiting the air flow of the filter...you should get the mount with a new battery tray to insure it doesn't flop around, gets proper radial clearance and correct position of the filter.
FYI...filter covers and their history:
Total waste of money from a performance perspective. They do everything they are not supposed to do. They lower flow by causing additional restriction, have no surface area for high volume, and are unnecessary if you use the properly rated element for the application.
From a filtration view, they can increase filtration efficiency in applications where the filter used has very poor filtration efficiency (ie: reusable/cleanable elements, K&N, AFE, etc). However, they do it will a substantially smaller surface area that has basically no capacity to speak of. It will also measurably affect your flow rate negatively from the increase of the restriction, because you are, in affect, adding an additional layer of filtration with no surface area.
Think about these numbers:
Surface area of Donaldson I use on the Tymar Intake: 4,000 sq in
Surface area of a K&N conical style: 975 sq in
Surface area of a filter cover: 150 sq in
Donaldson has 4 times the surface compared to the K&N, which is significant in its own right, but 270 times the surface area compared to the filter cover, making a filter cover nothing but a hindrance. Filter covers originated from reusable elements inability to filter the air of a dusty environment. Using a proper filter with a proper filtration efficiency and you don't need to worry about it.
Same thing with the guys using them to protect an open element using an improper filter from experiencing water mist. If you use a proper filter for the application that uses a hydrophobic (water resistant) filter media you don't need additional layers adding restriction and lowering flow to gain protection. Again, use a proper filter you don't need to worry about it.