I tone regularly, to manipulate the image tone and colour.
That is nice and can make beautiful images. Since your medium in this case is likely monochrome, this is not changing that, just changing the mono (one) chrome (color) a bit (from grey to something else).
I use filters to manipulate the spectral response, and vary the tonal relationships.
I tend to use filters to make the spectral response of the resulting image closer to what the eye actually experiences; thus correcting some imbalances in panchromatic film. I also use filters maintain sky density, lest the viewer be under the incorrect and potentially misleading thought that there was no sky. I also do use filters to manipulate sometimes (medY, deepY with orange citrus for instance does look nice at times; MedR for over dramatic sky; etc.). In these cases you could accuse manipulation, but I would say filtration is part of the monochrome medium toolkit.
I don't do a lot of soft focus work, but I know others who do, in order to manipulate the apparent accutance of the image.
Portrait photographers use soft focus to sell prints. Husbands and boyfriends use it to maintain relationships on good terms. This is strictly manipulation.
I take photos from unusual angles of view, in order to manipulate the apparent relationships between the elements in the scene.
I see the world from unusual angles and views, so not sure why that would be manipulation (ever laid down on the ground and looked up- I did this in 1984 at night while backpacking in the the San Bernardinos and was informed that there were artificial satellites following an orbit every 30 minutes)?
I have friends who manipulate photos by hand colouring them.
Almost as bad as those people who manipulate white canvas by painting colorful images on them!
I doubt anyone is misled, and I hope many viewers end up being better informed.
Manipulation can be used to mislead or misinform, but very few manipulations do that.
Adding clouds that likely would never exist in that setting or location, or that time of year, or generally at all, is manipulation, and only misinforms, for instance. This is often done for dramatic effect, but perhaps changes the image from a photograph to a work of graphic arts. Add the UFO while you are at it. Don't bother with the black helicopter because no one ever saw it or heard it.