There is a place for version control. I have used Visual Source Safe and derivatives in the past, as well as SVN; currently, I use Team Foundation Server, primarily for C# code.
For APL+Win, I find that a simple layered approach works for me.
1. In the first pass, simply calculate the checksum of like named functions; if different, then examine each in more detail.
2. I find that version control systems that have branching and merging capabilities not delivering their promise: manual interpretation is always necessary.
In general, having the like named objects in a database rather than in different workspaces simplifies the comparison.
On a more general note, I find that there is a concerted effort to introduce pseudo science in programming. In making this statement, I have in mind the proponents of programming methodologies (Agile, Waterfall etc.), testing frameworks (test driven development, mocking frameworks), and version control, of course.
It is interesting that no programming environment (interpreted or compiled) or other tool has as yet got the capability of certifying compliance (on a scale of 0 to 100, say) with either any programming methodology or testing framework or design (as in tiers) or DRY (Don't Repeat Yourself, i.e. design for code re-use) or design pattern or naming convention. This leads me to having some sympathies with the view point that programming, whatever its scale, remains a cottage industry; otherwise, we would surely have perfect code generators and translators (from one language to another). A while back, I used R: this language has a prime directive, namely, get the working code first. Everything else, like optimisation, runtime, etc. comes after. I've been using APL this way since I started.
Incidentally, I have been using the coexistence of differing versions of like named variables and functions to manage applications that have several deployment versions, namely, bespoke versions or simply versions that are using different databases. The deployment version is collated at runtime.