Hey thanks for the replies.
First of all, Pavtube is not free software, it is something you pay for, and when there are tools available to do these things for free, can make all the difference. Also, the purpose of this is for compression, too. Not everyone has the storage to store 1:1 rips. Other things to note:
Pavtube may have the ability to crack the protection within some Blu-ray discs however there are some releases it struggles with, especially by certain studios.
Pavtube gives you very little customisation and flexibility. You don't get anywhere near as many options -- if you want to make 1:1 copies, thats great, but if you want to compress, the quality is bad.
Pavtube is unethical - they mostly use spam to advertise their products. By purchasing the product you encourage spam much more in general by this company. 
Pavtube uses existing software and puts it's own skin on it, then charges extra
Pavtube has issues extracting some audio cores from certain releases, which means playing back may be impossible on the WD TV Live Hub as it doesn't support DTS Master on passthrough (and only passed through LPCM at stereo)
Pavtube also has very little in the way of updates. You may find that some releases aren't even recognised.
People know already that 1:1 rips causes issues with the Live hub. No DTS MA/TrueHD support and lack of support for PGS subtitles, therefore, you may find that movies with foreign parts do not display subtitles as they should and you may not even get any audio. By using the tools I suggested you can be sure as to what you want without being subject to such a basic interface whereby it causes the media to not even play back correctly.
Also, a few issues with MakeMKV:
MakeMKV takes a lot of time to encode, so unless you rip the content of the discs to the machine first then encode them, it is a case of ripping straight from the Blu-ray, which is bad, because it means the drive is locked and in use in the mean time. If something goes wrong along the way, you have to start all from the beginning, whereas if you copy with tsMuxerGUI first, you can take the disc out of your drive (prevents it overheating), and if the encoding fails you don't have to look for the disc first and re-rip it: the file is still on your drive. Overall, you save tme.
MakeMKV does not convert PGS subtitles to SRT - the only way is to run them through an OCR or download subtitles from another website. So yet again, no subtitles for those movies with non-English parts.
Not as much flexibility with the encoding as with RipBot264.
It is all running in one application: if it crashes, you lose what you are doing. You have to start again. If Ripbot264 crashes, the queue is kept and you can pick up where you left off reasonably quickly.
MakeMKV is primarily used for lossless backups. Like I said before, not everyone wants to have 30-50GB backups a time of their Blu-Ray content.
If you rush it by using a one program solution, the quality will be bad (unless it's a 1:1 copy), and you will have issues playing the content.
If you take your time to research, then copying becomes easy, and not so much of a bind. Quick, too. And the results are more perfect.
Does Pavtube even support 2-pass on MKVs? Probably not.