I’m not commenting on how a cylinder should or should not be prepped for assembly, but I am offering an explanation, from a surface science standpoint, of why one would use an aqueous soap solution in doing so. Although we may perceive a finished honed cylinder to be relatively smooth, from a surface science standpoint it is a very rough coarse surface (mountains and valleys) that is filled with a mixture of honing oil and extraordinarily fine metallic debris (think of the material making up the hard clay layer in the bottom of the honing tank or the bottom of an automatic transmission pan after years of use). We are kidding ourselves if we think we can wipe out all the honing debris that is trapped in the highly irregular metal surface by passing a spirits-soaked rag over the peaks. However, we go through our ritual with a spirits-soaked rag until it comes out visually clean and proclaim the surface to be clean, but is it?
Spirits are a low surface energy fluid that readily wets on most surfaces – both polar high energy surfaces and non-polar low energy surfaces, e.g. metal and plastics respectively. Water is a high surface energy fluid that wets high energy surfaces (clean metals), but does not readily wet most low energy surfaces like plastics or oil-contaminated metal. If we start wiping a freshly honed bore with spirits, we’ll remove some of the honing debris off the peaks and simultaneously dilute the honing oil that is present in the valleys. If we repeat the process a 2nd and 3rd time, we’ll remove slightly more debris and dilute the honing oil more. However, if the surface were truly clean at this stage it would be free of all honing oil contamination, and possibly all honing debris. A simple and easy method to determine if the surface is free of oil is to simply place a small drop of clean water (distilled) on the bore and observe it. If the bore were clean steel/iron the water will fully wet and spread on this high energy metal surface. If the bore has oil-contamination present, the water drop will remain as a bead on the surface and no further wetting will occur. If the bore is still contaminated with oil, wouldn’t it still be contaminated with microfine honing debris down in the crevasses, since there is no real driving force to move the debris out of such places?
Let’s assume for the moment that the wetting test with water confirmed that the bore is still contaminated with oil. At this stage of cleaning the large majority of oil and debris have been removed from the bore via wiping, yet our present conundrum is “how can we now remove the last traces of oil and debris from our oil-covered bore surface”? We know that water (high surface energy fluid) can’t wet oily metal, but what if we could somehow get water to wet the metallic surface, thereby displacing the layer of oily debris from the clefts and fissures of the honed surface. The answer to this situation is to add a good surfactant to water (dawn dish soap?), which dramatically lowers its surface energy and allows it to begin wetting the oily surface. By aggressively scrubbing with a fine bristled brush we are adding a significant amount of agitation, turbulence and physical contact which allows the soap solution to begin wetting and displacing the oil/debris remaining in the crevices. With continuous scrubbing the entire bore surface becomes wetted, thereby displacing the oil and its accompanying debris from the metallic surface where they can be washed away with fresh water. Following such aqueous cleaning, if the wetting test with water, described above, is repeated it should now confirm that the bore is oil-free.
The above rationale hopefully explains why one would consider employing a hot, high strength soap solution as a final step in bore cleaning. Your choice. My $0.02.