Why in most macro models technology is labor-augmenting? Take Romer's advanced macro book as reference. In it the Solow model,the Ramsey model and the Diamond OLG all contain the fundamental $A_t$  variable representing technological progress.
In all these models, technology affects only labor, that is:
$Y_t = F(K_t,A_t L_t)$

Now my question is why is such assumption so prevalent in these models. It seems to me that when we imagine technology as affecting output we think of the Northrop loom, the Bessemer steel, the container, the railroad. You know, stuff. All these seem to me to be mostly capital-augmenting technologies.
So why do we tend to assume labor-augmenting technology instead?
The mathematical reason, is that this happens in order for the model to have a steady-state in terms of growth rates: variables like Consumption, Capital, Income, grow at the steady-state, but grow at the same rate, so their ratios remain constant (and it is in this sense that this situation represents a "steady"-state). If they were to grow at different rates, their ratios would tend to either zero or infinity which is not very realistic, since it would imply that the economy tends towards one or the other "corner" situation.  

The mathematical proof can be found in Barro &amp; Sala-i-Martin book (2nd ed) , section 1.5.3, pp 78-80. Relevant and useful is also the discussion in section 1.2.12, pp 51-53.

For functional forms like (generalized, even) Cobb-Douglas, it is really indistinguishable (not separately identifiable), especially since we predominantly use the exponential function:

$$Y_t = A\cdot \left (K_te^{zt}\right)^\alpha \left (L_te^{vt}\right)^\beta = A\cdot K_t^{\alpha}\left (L_te^{(v+\frac {\alpha}{\beta}z)t}\right)^\beta = A\cdot K_t^{\alpha}\left (L_te^{wt}\right)^\beta$$

So strictly speaking in such a functional setup we can say that technology is also capital augmenting.

But since for other functional forms, the above does not hold, and so we must explicitly assume that technology is "labor-augmenting" for the reason stated previously, authors settled in labeling it as such in order to cover all cases, and when they want to keep the functional form unspecified.  

Regarding the conceptual issue the OP poses, which is insightful, a conceptual way out is to think of "Technology" more like "Knowledge". So "Knowledge" that goes into the machines, is part of the Investment that augments capital, while the other knowledge turns raw labor $L$ into human capital: essentially a production function with "exogenous labor-augmenting technology", is equivalent to a formulation that includes Human Capital instead of labor but where the investment in Human Capital is not subject to optimizing behavior but "automatic" (which points to Arrow's "Learning-by-Doing" concept of human capital accumulation).