First, it's not true that se is used with “one of the three subjunctives”; it's not used with the present of the subjunctive (that's a syntactic peculiarity of se more than anything else; if you replace se with the equivalent caso, meaning in case that, then you'd use the present instead of the future; the present and the future of the subjunctive mean essentially the same thing and neither has to refer to the future).
I assume you're only referring to se in conditional sentences (i.e. not an if in the sense of whether). Conditional senses don't necessarily express conditions (i.e., that in se A, então B, A is a sufficient condition for B). Extreme example: se bem me lembro, fui lá ontem.
Generally, three types of conditional phrases are distinguished: factual, hypothetical and counterfactual. The factual ones are used with the indicative. In this, it is assumed that the content of the propositions is true in the real world for the relevant timespan. Examples from Maria Mateus and others' grammar (6th ed., p. 706):
(1) Se está bom tempo, ficamos bem dispostos.
(2) Se a água atinge a temperatura de 100°C, (então) entra/entrará em ebulição.
(3) Se o narciso é uma flor, (então) pertence ao reino vegetal.
In all of these, you could replace the indicative with the future of the subjunctive, for instance:
(4) Se estiver bom tempo, ficamos bem dispostos.
And then we'd have, at least in principle, an hypothetical conditional, where the protasis refers to an hypothetical world, ‘epistemically inaccessible at the time of the utterance’ (ibid., p. 707). In practice, the difference between (1) and (4) is subtle. (1) can only be interpreted as a general rule or describing a habitual situation. (4) can be interpreted with effectively the same meaning, but it's information gathered from seeing this hypothetical world from the outside (if this makes any sense). (4) can also be interpreted as referring to some possible good weather in the future; in that case ficamos refers also to the future and can be replaced with vamos ficar.
It's not just the present that can be used:
(5) Se o Rui estava doente, a mãe telefonava-lhe todos os dias. [describing an habitual situation in the past]
(6) Se o Rui esteve (de facto) doente, fomos muito maus para ele. [assuming that he was in fact sick, we were very mean]
In informal speech, the indicative can be used even in hypothetical and counterfactual situations. This gives them more expressiveness, as you feel the events closer to you, as if they were really happening, rather than happening in an hypothetical world:
(7) Se te apanho [=apanhar], nem sabes o que te vai acontecer!
(8) Se o avançado tem apanhado [=tivesse apanhado] a bola naquela zona, era [=teria sido] uma situação muito complicada para a defesa.
The counterfactual case (where the imperfect is used), is less of a problem because it's easier to distinguish. Looking at your sentence, it seems to me that you want to express a counterfactual situation. Here you have to use the pluperfect:
(9) Se as tivessem comido, tudo teria sido normal.
The one you gave (with tinham comido) is only acceptable in some registers. To me it sounds provincial, and so does (8). (7) is idiomatic.