The tours are more about transport that having a guide tell you all about the history of the place. The limitations are that you arrive an move on at the pace of the tour rather than your own pace.
When I did Valle Acoris https://psamathe.net/valle-del-arcoiris-chile/ plenty of time to wander slowly through (though Hierbas Buenas that seens “bundled-in was a bit dull and I should have just sat out in the sun for the broef visit). Though it was acually quite useful having the “guide” to ask detailed geological questions about the formations and colours (something you don’t get when visiting independently)
Valle de la Luna https://psamathe.net/valle-de-la-luna-atacama-desert/ tours seem to run on a rough timescale so you end-up arriving at the mirador around an hour before sunset (which is why they start afternoon). Plently of time to stop and photograph what you want, it’s not a rush to get round in time; the “guide” was pretty non-existant and I just went where I wanted when I wanted (within the constraints of the paths as you are not allowed to wander anywhere - the environment is protected).
There are bike (pedal bike) rental places in San Pedro though I have no idea what it’s like to cycle outside the town. Valle de la Luna is actually quite spread out in that you visit caves at the start, then further in to the valley itself (which is large) then travel back right round to the opposite side to the sunset mirador.
As you are coming from the Bolivian Salar, people say that the Chilean lagunas and hot springs are not as good as the Bolivian ones (that you will have seen on a 3 day Salar trip). Just repeating what others have said as based on this and having seen plenty of lagunas (on the Bolivian Salar) I didn’t bother with the Chilean ones instead visiting places like Valle Acoris, Valle de la Luna which are very different from Bolivian Salar lanscapes.
In a general context, I also dislike “tours” but they can be a low cost way to get to places were there is not a lot of public transport. In some areas I “took the tour” but on arrival said goodbye to the tour or asked what time the bus was returning and said I’d meet them back at the bus then. Don’t dismiss tours just because they have the label “tour” (which sounds touristy) but think about what you want to see and the best way to achieve that.
Remember that the Atacama is a hot and dry desert. When wandering around it just feels (to me) like a pleasant climate (I love heat) but it can be dangerous so if you do walk/cycle/whatever alone make sure you take appropriate safety precautions.