Hi Steve,
On the topic of your first point, TiddlySpot PHP... TiddlySpot uses a program on the server to save the Tiddlywiki file. When you press the save button on your tiddlywiki, it makes a call to the server side program to save itself on the server.
The team is saying they need to review the server side script, apparently written in PHP. I reviewed a variation of that script. In my opinion the version I reviewed is adequate for a hobby site. I would want a lot of enhancements to it for anything serious (but that's just my opinion).
On the second point, there are really 2 issues in the one point.
First is that anyone with access to save a tiddlywiki on your site could modify the javascript that makes tiddlywiki work. Since tiddlywiki is giving you the ability to edit the javascript within the tiddlywiki, it is easy for anyone who has access to it to modify and save it so that it affects the next person to view the tiddlywiki.
Second is the issue of cross-site-scripting (XSS). That is, because the core of tiddlywiki can be modified by anyone who can save a tiddlywiki, they can have it call outside scripts (this is how things like the discus plugin work). The problem is, like the first part, once one person modifies it, it is affected by everyone else who uses the tiddlywiki.
In summary, tiddlywiki requires a very high level of trust in everyone who can edit a tiddlywiki document. As such, it may not be appropriate for environments where you shouldn't place a high level of trust in your users. Like say the students at a University.
The node.js version of Tiddlywiki might be a bit better in addressing the above, but it would still need to prevent the users from saving any javascript.