Until Konami actually patch this (lol) here is a simple reshade preset to make the game look a bit better. The bilinear filtering is still there, but with this it's a lot more bearable imo.

-Download Reshade from here - https://reshade.me/
-Open the Reshade_Setup file and click on "browse", then choose "METAL GEAR SOLID.exe" in the game's folder.
-Select DX10/11/12 as the API and click Next
-Click Next/Skip as there will be no presets to install
-Make sure to select the "RSRetroarch by Matsilagi" package.
-The two main RSRetroArch files/effects to install are "CRTFakeLottes.fx" & "ImageAdjustment.fx, although you can download all the files to try out different CRT effects.
-Click Finish.

Then run the game. Press the "Home" key to bring up reshade, skip tutorial and enable "RA_ImageAdjustment" and "CRTFakeLottes".
Below in the shader settings, under "ImageAdjustment.fx" change Horizontal Overscan to 6, and Vertical Overscan to 7. This will get rid of the bottom and top black borders. Because the game is using bilinear filtering it wont cause any shimmer as there aren't any integer scale pixels that Konami can destroy.

under "CRTFakeLottes.fx" settings, change "CURVATURE" from "1" to "0" if you don't want the screen curvature effect.

I really hope Konami do actually patch this to remove the filter, but knowing their track record they probably wont. Even if they do and add their version of a crt filter or scanlines, it most likely wont be as good as what we can get with reshade, so it's worth trying out all the other CRT shaders offered with the RSRetroArch package.

Screenshots really do not do this justice, as the scanline filter only appears correct when viewed in fullscreen.