1. Should they be "the second (were) ... uses the subjunctive form for this non-factual situation" and "the first (was) uses the indicative"?
2. If the "was" one is also used for a non-factual situation, then how can we say it if we want to use "as if" to describe a situation happening in the past which we think it may be factual?
The subjunctive "were" in an "as if" (or "as though") construction does not by itself indicate that the situation did not happen (or is not happening) in the way described by the "as if"-clause. Traditionally (see H. F. Fowler, for example), "as if"-constructions are reductions of longer constructions containing conditionals.
She felt as if she were being followed. = She felt as [she would feel] if she were being followed.
In other words, if she were being followed, she would feel a certain way, and that was how she felt. To indicate counterfactuality, i.e., that the situation referred to in the "as if"-construction did not happen, we should technically (according to the traditional analysis) use the past perfect (cf. Type 3 conditionals).
She felt as if she had been being followed. = She felt as [she would have felt] if she had been being followed.
In other words, if she had been being followed (counterfactual supposition), she would have felt a certain way, and that was how she felt. Interestingly, because we can't tell, with "were," whether the situation happened or did not happen, is happening or is not happening, we can add "really" in either case. That is, "really" need not be viewed here as being in grammatical conflict with subjunctive "were."
She felt as if she were really being followed. /
She feels as if she were really being followed.
In actual practice, I do not have the guts to go with "were" in the present-tense case when there is a belief in factuality, because there is a strong tendency to assume that "were" indicates counterfactuality, even when it is, strictly speaking, neutral. In that case, I generally shift to "as though" and use the present tense:
She feels as though she is really being followed.
Technically, however, "as though" is just "as if" differently phrased, since "though" was used historically to mean "if." On a final note, these constructions are all rather formal. Despite my love of grammar, I do not wish to pretend that I am immune from saying "She feels like she's being followed." On the contrary, that is the first utterance that would come to my tongue. Everything else is editing.
