Trouble with the audio track in audio blu-rays

[Makri]

Hello everyone!
I have a selection of Audio Blurays which I want to rip and store on a NAS for ease of use. They will be streamed through Plex to my Apple TV 4K and then played out through a stereo system I have at home. I am planning on expanding to a home cinema (7.2.4) in about a year, however. But, these audio blu-ray's usually have 4 audio tracks (2.0 LPCM Stereo, 5.1.4 Dolby Atmos, 5.1.4 Auro 3D and 7.1 DTS-HD MA) in them, and when the audio is playing, the menu is left on screen with possibilities of changing sound codec and chapter (or track in this case). Now, when I am making the MKV's using MakeMKV, I get some odd behavior:
First of all, MakeMKV usually reports two titles. So for almost all of them I get Title.00 and Title.01. Even though there is actually just a menu and 4 sound codecs for 3-9 tracks (depending on which one I put on). Even weirder is the reported audio, where this is the usual:
Title 1:
AC3 Stereo (This usually has no sound)
AC3 Stereo (This usually has no sound)
TRUEHD 7.1
AC3 5.1
DTS 5.1
DTS 5.1
Title 2:
DTS 5.1
DTS 5.1
PCM Stereo
AC3 Stereo
AC3 Stereo
I know that there are a folder on the disk containing all the music on the disk, for download/use on media players. But that is in a completely separate folder from the movie and shouldn't be included in MakeMKV selection pane, or?
As you guys can see, it is simply a mess when I try to make MKV's out of these. I wanted to be able to just select the movie and codec, not this ballet of intricacies.

[Woodstock]

If your target is Apple devices, you probably should become familiar with ffmpeg, and use it to convert the audio tracks to AAC. Apple doesn't like AC3 (they do not want to license it), so AAC is the most compatible.

[Makri]

If your target is Apple devices, you probably should become familiar with ffmpeg, and use it to convert the audio tracks to AAC. Apple doesn't like AC3 (they do not want to license it), so AAC is the most compatible.

Well, the thing is that I don't really want the AC3 track at all. It doesn't play on my win10 computer either, for what it's worth. I simply want the blu-rays to be able to run through plex or whatever and enable me to choose between the 4 original tracks. I also struggle with seeing why there is two titles on the Blu-ray disc since it is essentially one long concert.

[Woodstock]

What are you using as a player on Win10? I have not had issues with AC3 on Windows, but I also haven't tried to use the Win10 "movie" app in a while.

[Makri]

The thing is, only 2 of the 4 AC3 tracks is without sound and the others play just fine. I believe maybe the four original tracks is encoded in all of these different audio tracks and I should explore the options on merging them, It doesn't seem like Handbrake can do this though.