I installed the mods in the guide with Windows 8.1. I did not install all the optional mods, but I did install most of them. I did not use fast travel since, as mentioned in the guide, it is can cause problems unless used quite infrequently. Fast travel causes problems in all the Bethesda games. I did not have any significant problems with CTDs. I don't know about Windows 10 effects. Other users have installed the game with Windows 10 and they have not reported the same in game problems you did. The Fallout 3 engine is certainly less robust with Windows 10 than with previous versions. I'll be installing Win 10 very soon and I'll have a better idea of what it affects.
The container in Springvale has been reported in the forums. At least one of the TWPC patches removes it (the largest one), and I also thought it was mentioned in the guide. I initially installed with only the bash tags for major mods like FWE using the tags in LOOT. There aren't compatibility problems with most of the mods in the guide; they don't affect other mods at all. In my games I don't expect to get all the compatibility problems fixed; it would be much too time consuming. I live with some compatibility problems like a few incorrect item stats but not with problems that cause CTDs.
I didn't test AWOP myself, but several forum users reported they used it and did not have problems.
The installation instructions that allow options should not affect CTDs or similar problems as the choices provide very small changes. For any mod that isn't labelled optional I have tried the options in the guide.
I'll look at the CTDs you saw and see if I get them also.
A lot of users were interested in Fallout 3 to play before Fallout 4. Now that this has past there aren't as many users trying out the mods, finding problems, and creating patches.