Search in project short answer: yes, it works.
Unless some other problem crops up, we now have a workable answer.
Search in project works for me if I make a project folder which contains links to the files in the project where the links are created in bash (via terminal -- iterm2 in my case). I used
ln -s full/path/to/sourcefile full/path/to/targetfile
Using full paths would allow running from anywhere, regardless of where the files involved actually are.
Using apache as an example, the bash command looks like this
ln -s /private/etc/apache2/extra/httpd-vhosts.conf ~/Documents/2-apache-b/httpd-vhosts.conf
I opened the directory 2-apache-b in TM2 and added it to favorites. A search for ServerName, for example, found all instances of ServerName across the set of files in 2-apache-b. That is, it looked like all occurrences. There are a lot of instances in the files I searched and I didn't verify "all". It looked reasonable, though.
If I had a hundred files to set up this way, I wouldn't want to do it. But if I'm adding a few files to a directory, or combining two directories into one for editing, or, as in this case, just combining four commonly used files, the utility of searching well outweighs the setup.
A script reading from a list of files plus the target directory would be reasonable. A bundle adding a few files together would also be useful.
--Lewy