the problem is not that android is somehow not "inclusive", it's that android allows vendors to ship a modified browser for whatever silly reason they want to, and the vendor never releases any updates for the modifications they provide.
unless Jolla is going to take over control of the phone and ship software updates directly to consumers without involving the handset vendors, they aren't going to solve the problem.
Yes, while I have no official word (I'm just a fan), I think this will be the case. As long as it's an official port done by Jolla, Myriad/Alien Dalvik should be available.
Note, that if you use the 3rd party port of SailfishOS on your Nexus5, it doesn't come with the Myriad/Alien, Android compatibility layer.
The community however has developed and released sfdroid: https://www.youtube.com/watch?v=xOU8fa0ZLT0
I've been using SailfishOS for almost two years, and I confidently say that underneath the GUI, it is just a regular GNU/Linux system[1].
Why do I bring this up? Jolla, and the community are developing a more inclusive mobile OS (that has Android app compatibility, and can be ported to Android devices relatively easily using libhyris[2]). I'm hopeful that it will help minimise the hackery described in the article.
For example, SailfishOS ships with Gecko engine v31 at the moment (soon to be updated...), QtWebkit, and (soon, after the port to Qt5.6 is complete), QtWebEngine (Chromium).
I'm hopeful that more Indian (and Chinese) phone manufacturers can start contracts with Jolla. I'm not aware of any software houses (as opposed to internal) that customise Android for your device.
[1] glibc, systemd, BlueZ, Pulseaudio, gstreamer, connman, Telepathy, Python, gcc, Qt, etc.
[2] https://en.wikipedia.org/wiki/Hybris_%28software%29