Ah, yes, another person with the includefrom problem. Sigh. I just looked at the import.sty documentation, and realized that its use is simply going to break the makefile in spectacular ways.
Using subdirectories for included files has never been well-supported by the makefile, and unless we can change things about "make" itself (including file path parsing, inconsistent backslash escaping, and any number of other oddities that most people simply never run into), that scenario never will be well-supported (or even supported at all).
I know it's sort of an ugly answer to give, but the only way to really use the makefile that works is to put everything that is editable into the same directory. Imports of non .tex files (e.g., .sty files) are supported from anywhere in LaTeX's path, but .tex files pretty much need to be right there with the main document file. Otherwise, as you have noticed, everything blows up.
The reason the .tex file is automatically included in the .d file is that if you change it, you want to trigger a rebuild. Taking that dependency out will break that. The only real solution is to get the path right.
I just poked around with what includefrom does to the log output to see if this case can be detected. Unfortunately, the path to chapter1 is only listed in exactly one place in the log file, and that place is unreliable as a source of path information (non-informative and lossy, since we would have to cross-reference ./main.aux with chapter1/main.tex using more than 2 input sources - really, really hard to do in this code). If the .aux file were to have some indication of the full path, that would be different, but it doesn't.
So, this is just not supported. In order to make that clear, perhaps I should detect the import.sty package and bail out with a meaningful error. Otherwise this will continue to confuse folks.