Okay, first I thought it was an issue with my install, so I installed the template on another site and I am still experiencing the same issue on both sites...
Both sites have:
Joomla 3.8.8
Gantry 5.4.23
Denali 1.0.1
Google Chrome Version 66.0.3359.139
On the Base Outline, when I go to Particle Defaults, many of the particles I can only edit certain fields of that particle - for example, the Simple Counter, I can't change the date or the month (drop down selectors) other particles are completely blank (title is there, but no parameters).
I also was informed that Denali supports headroom for a fixed header/menu, but both installs had no headroom Atom present.
For all particles in the right column, CSS Classes field is uneditable, none of the dropdown selectors work, and none of the input selection buttons work. This also happens on the Base Outline -> Page Settings
Particles that are completely missing their parameters:
Left Column
Right Column
Block Content
Popup Module
Carousel
Pricing Table
Case Studies
Search
Grid Statistic
Showcase Slider
Image Grid
Simple Content
Info List
Slider
Video
Particles that cannot be edited in Particle Defaults can be edited on the individual Layouts. On further investigation, this behaviour seems to only happen so far in the version of Google Chrome mentioned at the top of this post, tested in Safari on Mac OSx El Capitan and functionality works, but still has missing parameters for the Particles mentioned in the above table. Will also double check with IE, Edge and Chrome browsers on my PC a little later and update any findings.
regarding Particle Defaults, we decided to only leave the Title and the option to disable/enable the particle globally for most particles, so what you're seeing is expected. Since we introduced Inheritance/Copying of particles/sections, the Particle Defaults became redundant and we may even remove the tab completely sometime in the future. Also, the page itself became very long with all options present and a lot of users struggled to correctly use Particle Defaults and individual overrides. The best approach is to set up the desired particle individually in one of the outlines and if you then wish to use it in other outlines, you can inherit/copy it and edit as needed. Practically there is no more real need for Particle Defaults.
Headroom is not included in Denali to my knowledge.
I will check the CSS classes thing in a little bit and post back then.