Okay, I feel a little better about what I said though I still don't have a concise citeable explanation of it (like out of a chemistry text book).
Phosphoric acid is no worse than hydrochloric acid, both of which are commonly used in chemistry and industry as a reagents. As long as you are wearing nitrile gloves, eye protection and proper ventilation you'll be fine. The hamon line that you see is from the acid interacting differently with the martensitic steel (the hardened edge) and the pearlitic steel (the soft spine).
The acid creates either Fe3O4 (black rust) or in the case of phosphoric acide FePO4. The orange rust you see is Fe2O3. Ferric Oxide (which is always present on iron that contacts air, as Iron is not stable and will immediately interact with oxygen creating FeO (ferric oxide)) can combine to make either Fe2O3 (red rust) or Fe3O4 (black rust, a further oxidization of FeO). This explanation is from:
http://www.finishing.com/95/49.shtml
"Hello, perhaps I would be able to answer this question since I majored in Chemistry. First off, as was already explained, rust as you probably are familiar with it is an iron oxide. The red/brown stuff is Fe2O3, or Iron III Oxide with a +3 charge on the iron. However, being a transition metal, iron may also exist with a +2 charge. Oxygen under ordinary conditions only exists with a -2 charge. This means that you can have FeO or Fe2O3. In certain mineral structures you can also have Fe3O4 (This is also an Iron III Oxide.) FeO and Fe3O4 are usually black. Unfortunately, this is not the whole story. Sometimes, molecules of the same chemical can be arranged in different ways or in different structures. Usually one of a few of these forms will predominate, however atoms arranged in different ways will effect light in different ways. For example, you are probably familiar with diamonds and graphite. Technically, they are both made of nothing but carbon atoms. But most people would rather wear a diamond on their finger than a chunk of graphite. Actually, Fe2O3 can exist in a black state, the structure known as Black Alaskan diamond. If I am not mistaken it also plays a role in giving color to other precious gems but since these gem structures involve more than a single type of molecule I will avoid further discussion. If you want to know if you have FeO or Fe3O4, you can try to put a flame to it. FeO should become rust like you know it if it is forced to react with more Oxygen. Fe3O4 on the other hand already has given up all the electrons it can and actually there is something else going on with it that I will not explain. Suffice it to say that 2 of the irons in Fe3O4 are +3 while one is +2, but due to something called resonance the charge is distributed."
It interacts differently with the martensitic steel and the pearlitic steel (I think, further reading necessary to verify as this is just hypothosis with no real citable sources) because the martensite is a much tighter formation that leaves less open iron at the surface. The pearlite is a much looser softer formation that leaves a lot of interstitial spaces on the surface where iron can be taken up by acids and the rust forming process.
One of the problems with patina's is that it creates a rough surface that has a lot more surface space for salts (sweat, blood) and moisture to collect in, which creates a situation that counteracts a lot of the corrosion resistant properties of the stable 'black rust' layer, or patina. That's why I try to keep my khukuri's at a high polish after acid etching them, using the etch as a way to uncover the underlying heat treatment. The polish leaves a very smooth surface with very few pits, scratches, or textured spots for salts and moisture to collect in, reducing the likelyhood of heavy rust from environmental conditions. I know that you can polish a blade and leave the patina as seen on japanese swords, but I've never seen an article or description of how to do so.
Some worthwhile reading:
http://en.wikipedia.org/wiki/Martensite
http://en.wikipedia.org/wiki/Austenite
http://en.wikipedia.org/wiki/Pearlite
http://en.wikipedia.org/wiki/Industrial_etching
http://en.wikipedia.org/wiki/Phosphoric_acid#Rust_removal
http://upload.wikimedia.org/wikiped...Table_of_Elements_showing_Electron_Shells.svg
http://en.wikipedia.org/wiki/Electron_shell