FFMPEG (and x264 at its core for bluray) can easily handle interlaced video. The latest version of convertx2hd is deinterlacing 1080i files when it doesn't need to. Can you please fix so that TFF is sent to FFMPEG with forced interlacing for interlaced sources. This will make MBAFF encoding for interlaced sources and not damage the video with deinterlacing. Maximum bitrate is too high as well at 48mbps for bluray. Please set maximum bitrate to 40. Average bitrates are around 15 for an auto small project. This should be increases to 25 to help with black fade transitioning. Color primaries, transfer characteristics and matrix coefficients should also be set at Rec709 (BT709) for full compatibility for bluray. Also, can we choose AC3 bitrate?
These small changes will go a long way to making output even better, unless you have option to take our encoded files as is and make menu around it.
Attached is a verified bluray mediainfo for how 1080i should be handled. You should use the --blueay-compat switch for ffmpeg as well as --vbv-bufsize 30000 --vbv-maxrate 40000 for bluray. Doesn't seem like you are.