Caravaggio might have painted the hair highlights separately, or used relatively small bristle brushes to paint a few separate hairs simultaneously. In his time, these details were usually added after the bulk of the work was done (the highlights in general were applied in the last stage).
It was still very common in the 17th century to 'draw' that much detail, especially so for surfaces that demanded that extra attention to create their 'material rendering'.
To get a better idea of the technique used, here are a few more examples of hair highlights done by Caravaggio:
The Musicians [detail], 1597
Supper at Emmaus [detail], 1601
Saint John the Baptist in the Wilderness [detail], 1604/05
Especially in the second example you can see how the hair is built up: there is a dark, warm ground or imprimatura serving as the main colour; to this, swift brushstrokes of a darker brown (burnt umber?) were added to give more shape to the hair; a lighter, blond colour (a yellow ochre with lead white?) is used to bring out locks of hair that catch the light.
These last, lighter tones were painted with mixtures of pigments and oil of varying degrees of fluidity, but overall there is a distinction between complete locks of hair, and highlights on single hairs.
Here you can also see how some lighter locks have received individual highlights, painted separately (esp. directly to the right of the ear).
If you compare this with, for example, the following portrait by Albrecht Dürer from a century earlier:
Albrecht Dürer, Portrait of young Venetian woman [detail], 1505
You can see that, while the application of Caravaggio has become freer, the procedure is still very much alike: three loosely applied, lean, and possibly somewhat scuffed basic shades (of which one is likely a ground, imprimatura, or grisaille), over which individual strands were painted with a more opaque paint.
The hair in the following portrait by Van Dyck, painted not a decade after the death of Caravaggio, shows a similar structure, but is applied in an even looser way, and—except for the highlights—completely wet-on-wet:
Anthony van Dyck, Saint John the Evangelist [detail], 1618/20
In all these instances, it seems to me that the highlights were painted in an opaque paint with tiny brushes over a more loosely and thinly applied series of shades.
I believe that Manet was usually painting wet-on-wet. It was the preferred method of the realists and impressionists.
The general structure of painting, even here around the eye, is similar, though. You can see how the white of the lit side of the nose is of the same hue as that of the eye, and how these highlights around the eye lay on top of a very lightly applied dark brown, possibly part of the initial sketch, through which the texture of the canvas shows:
There is the dark ground; a darker hue with which the eye's contour and the pupil were painted (possibly as part of the initial sketch); the intermediate greyish flesh tone (mixing in with the former darker brown along the top edge of the eye); a light flesh tone, with which the lit parts of the face are painted; and an even lighter and semi-translucent white with which the white of the eye is painted.
While scratching has been used to etch detail into the still wet paint (notably by Rembrandt), I don't believe these are scratches.
Despite the details pointed out in the paintings not being glazings (and having revised my answer after this was rightfully pointed out), I think the answer to your titular question is still nevertheless 'glazing': if transparent highlights are desired in oil painting, the only viable option is 'glazing', since that is the application of transparent layers on top of existing ones.
Images that were added later to the question have (again) complicated the matter, but I think (the altogether different) brushstrokes like the central, vertical ones in this cropping below..
John Singer Sargent, Mary Crowninshield Endicott Chamberlain (Mrs. Joseph Chamberlain) [detail], 1902. Source.
..are simply quick brushstrokes with opaque paint, probably painted with a rougher bristle brush or a brush the artist knew would have this character and give these slightly separate lines, e.g. a dried out brush that Singer Sargent knew would give this texture.
The illusion of transparency is due to the textured way in which the paint is applied to the canvas—the brush likely having been handled in a grazing way.
