Let me sum this up and, I hope, make it completely clear:
It is a goal/requirement of KoLmafia's Relay Browser that it not break KoL's interface. So, when the rollover timer did not show up in the charpane of the Relay Browser because we changed the HTML of the page, I fixed that, and that KoL feature now works just as well in the Relay Browser as it does in vanilla KoL. Similarly, when I became aware that KoL had a "remember my frame widths" option which didn't work in the Relay Browser because our behavior as an HTTP proxy was inadequate, I fixed that, and that KoL feature now works as well in the Relay Browser as it does in vanilla KoL.
In other words, it is a goal/requirement of KoLmafia that we do not REMOVE functionality from the KoL browser experience. We can ADD things - some of which are later implemented by KoL itself in different (and, depending on your taste, inferior ways). For example, we had Stationary Buttons before KoL had a CAB, we had up-arrow and shrug links in the charpane before KoL added more limited versions of those, we had "use" links upon item acquisition, before KoL added a right-click popup menu to acquired items, and we had counters in the charpane before KoL added timers. In some cases, KoL's implementation of the feature conflicts with KoLmafia's - CAB vs. Stationary Buttons is a prime example - but we do not override KoL's feature; we look at KoL's configuration options and only put in our feature if you have disabled KoL's feature.
Now, third-party addons that, effectively, run in the browser - Greasemonkey (which really is in the browser), and KoLmafia Relay Scripts (which are between the browser and KoL, but are otherwise similar) - can drastically modify the KoL interface and completely change the whole experience. They may or may not work with arbitrary KoL interface options; it is a goal of KoLmafia itself that it work, regardless of how KoL is configured, but if you install optional interface-modifying add-ons, it is not KoLmafia's job to force them to adhere to that same level of compatibility. As an example, consider ActiveChat. Before KoL came out with mchat.php ("Modern Chat"), this was layered on top of KoL chat and gave you tabbed chat. In order to use it, you had to set a collection of KoL char settings Just So.
And now, it appears that Guide requires a particular KoL Interface option - "remember my frame widths" - to be set Just So. In particular, off. The fact that it used to work regardless of that setting because KoLmafia had a bug that prevented that option from working does NOT mean that when KoLmafia fixes its bug and the KoL option now works correctly in the Relay Browser and Guide no longer works unless you have that KoL setting off (as it does, according to Lxndr in the Guide thread), that this "negative impact on Guide functionality" is a KoLmafia bug.
It is not a KoLmafia bug. It may not even be a Guide bug. It just means that if you want to use Guide, you have to configure a particular KoL option in a particular way, much as Active Chat required you to configure particular KoL options in particular ways.
I have nothing more to say about this Bug Report.