As @jhutch pointed out, it happens even when installed to the root of the domain. With a clean install of IPS4 to the root of the domain, if you set Pages as the default app, then forums are given the url x.com/forums/forum/xxx-name. I would also appreciate clarification on the questions I asked... This site has the forums set as the default app. That's the difference.
This is related to which app you have set as the default. The issue doesn't appear on this community because forums is the default app, so the forum URLs are x.com/forum/xxx-name and x.com/topic/xxxxxx-name. If you set any other app as the default, then the forum URLs are prefixed by /forums/, and you end up with x.com/forums/forum/xx-name and x.com/forums/topic/xxxxxx-name. This is a change from v3. My community is set to have IPC as the homepage, but the forum urls remain x.com/forum/xx-name and x.com/topic/xxxxx-name. To me, this makes more sense than the redundant /forums/forum/ structure. v4 does have a nice interface to manually edit how your URLs appear, but it's also accompanied by a warning.
So, if I change the URLs to /forum/xxx-name, the software is unable to 301 the /forums/forum/xxx-name URLs? Well, that would really devastate my community's indexing. Okay, I can write an nginx rewrite (or .htaccess if that's your flavor), but this is way above an average user's ability just to restore v3 behavior. If I upgrade my community, will the old /forum/xx-name URLs be properly forwarded to /forums/forum-xxx-name? I can't test the upgrade until the next beta (all the bugs I've encountered have been fixed), but based on my clean install /forum/xxx-name URLs get 303 forwarded to /forums/forum/xxx-name... which I had to look up (303- See Other) and seems less preferable to a 301.
Off topic, but I just noticed: is there really no way to preview your post's output before posting it? Is that a gear icon to insert a quote?
On my live board running IPB 3.2.3 with the Similar Topics hook, a thread with 1036 replies took .1455s to execute with 15 queries. A thread with 14,082 replies took .1236s to execute with 14 queries. Those numbers seem reversed based on the size of the threads, and obviously can and will vary, but they are pretty average for me.
Just to add some anecdotal evidence: I sell my ads on a per month basis, with no guarantees or analytics for clicks or impressions. All but one of my current advertisers use a flash banner, and that's how they're going to advertise for virtually ever. They have no desire to (pay someone to) redesign their banner. If Nexus allowed swf banners, it would substantially lower my overhead in terms of billing/arranging/managing ads.
Ultimately I think adding the feature helps many of us monetize our communities, and adds no bloat for users who don't need/use flash banners.
EDIT (didn't see .time's psot): Calling flash a scarce plugin is an exaggeration. I agree with you whole heartedly that flash is dying and should die, and HTML5 is a preferable alternative. However, the choice of what medium an ad uses isn't mine. If my advertisers want to use a flash banner that limits the number of people who can see it, I have to try and support that whatever way possible.
Currently .swf banners can't be uploaded as advertisements in Nexus. The only work-around (found in this topic) is to manually enter the HTML in the ACP, but this doesn't allow users to purchase ad space and upload a .swf.
The only reason to not allow flash ads is security, but that should be a decision for site operators to make.