I tried IDM and 4k Video Downloader.
While IDM gives the MKV option consistently at 480p, but it isn't consistent in offering MKV download option at 360p.
4k Video Downloader
While it does offer MKV option at 360p for all youtube videos, but it's download mechanism isn't very reliable. It often stops downloading the videos mid-way and one is forced to start the download for such videos all over again.
Aren't there other software alternatives to download youtube videos in MKV format at 360p?? (P.S.: I'm using Windows-7 32-bit version)