One case is more general than the other.
The log likelihood for multivariate normal distributed errors is related to a term $$-\frac{1}{2} \log \left(\vert \mathbf{\Sigma} \vert\right) {-\frac{1}{2} \mathbf{\epsilon}^T \mathbf{\Sigma}^{-1}\mathbf{\epsilon}} = -\frac{1}{2} \log \left(\vert \mathbf{\Sigma} \vert \right){-\frac{1}{2}\sum s_{ij}\epsilon_i\epsilon_j}$$ where $\mathbf{\Sigma}$ is the covariance matrix, $s_{ij}$ are the entries of it's inverse, and $\mathbf{\epsilon}$ is a $1$ x $n$ vector with the residuals/errors.
note that this is not a simple sum of squares $\epsilon_i\epsilon_i=\epsilon_i^2$ but also contains mixed product terms $\epsilon_i\epsilon_j$
If $\mathbf{\Sigma}$ is diagonal ($\mathbf{\Sigma}_{d}=0$ for non-diagonal entries) then this reduces to a simple sum of squares. $${ -\frac{1}{2} \log \left(\vert \mathbf{\Sigma_d} \vert \right)-\frac{1}{2}
\mathbf{\epsilon}^T
\mathbf{\Sigma}_d^{-1}\mathbf{\epsilon}} = -\frac{1}{2} \sum \log \left(\sigma_i^2 \right) {-\frac{1}{2}\sum\frac{\epsilon_i^2}{\sigma_i^2}}$$
or even more simpler when $\mathbf{\Sigma} = \sigma^2\mathbf{I}$ $$ -\frac{1}{2} \log \left(\vert \sigma^2\mathbf{I} \vert \right) {-\frac{1}{2}
\mathbf{\epsilon}^T
(\sigma^2\mathbf{I})^{-1}\mathbf{\epsilon}} = -\frac{n}{2} \log \left(\sigma^2 \right) {-\frac{1}{2\sigma^2}\sum \epsilon_i^2}$$ which is maximized by changing $\beta$ and $\sigma$ and independent from $\sigma$ the maximum occurs when $\sum \epsilon_i^2= \sum (y_i-\mathbf{x_i}\mathbf{\beta})^2$ is minimized.
So only for the second and third case do you have a plain sum of squares expression. In the first case there are also cross terms, and more importantly there are more parameters to estimate (ie. all the correlation terms in the matrix $\mathbf{\Sigma}$ ) That is what is meant in the statement
if normal likelihood loss is specified, then the covariance term is trained as well.
If you wish you could transform/rotate the variables and then the first case could be expressed as the second case with a sum of squares. But then it becomes a bit a semantic issue. You would still have to compute more parameters (for the transformation) and you are not using an ordinary least squares loss function.
Q1: The multivariate normal likelihood is more generally a second order polynomial of the error/residual terms (with terms $\epsilon_i\epsilon_j$ for which not necessary $i=j$). Only in the special cases (independent errors) does this polynomial only contain the square terms (with $\epsilon_i\epsilon_j$ and only $i=j$)
Q2: The covariance term is the covariance term in the multivariate normal distribution that is used to express the errors. The covariance term allows to model errors that are dependent/correlated. In the case of time series this is probably correlation between errors of nearby time points, since it would be difficult (if possible at all) to estimate the entire covariance matrix $\mathbf{\Sigma}$ when there are no imposed restrictions. (a common model where error terms are considered to be correlated is a mixed effects model, see for an intuitive example https://stats.stackexchange.com/a/330097/164061)
Q3: Training the covariance terms means that the covariance terms are estimated in addition to the parameters of interest (e.g. a sample mean), as part of finding the minimum of the likelihood function. The covariance terms are nuisance parameters.
It may also be that a single measurement $y_i$ is a vector and that the errors in that vector are considered to be correlated.