Does it matter whether as goes at the beginning or in the middle of a sentence?

One understands naturally, so to speak, that "only" means "did nothing else but"; however, the naturalness is to be placed on the count of the logic of what the remainder of the sentence tells us, not the position of the adverb, this being so because in this position one possible interpretation, "he watched TV but watched nothing else", even if it doesn't make sense, intrudes on the deciphering that goes on as we read. It is true that the unambiguous place of only with respect to eliciting this latter meaning would be right before "TV". So, I feel a little as you do: the use of "only" as it stands does not appear entirely satisfactory.

This would find further explanation in CGEL 8.117

Position and focus
Whether restrictive or additive, focusing subjuncts are most frequently placed at M [right behind the main verb] unless the item focused is the subject, a part of the subject, or an auxiliary verb. But with the subjunct at M, one has the choice of focusing the main verb, another part of the predication, or the whole predication. Compare the following, […] with the restrictive only:

• John could only <SÈE> his wife from the doorway.
  (eg he could not talk to her)
• John could only see his <WÌFE> from the doorway.
  (eg he could not see her brother)
• John could only see his wife <FROM THE DÒORWAY>.
  (eg he could not see her from further inside the room)

I believe that the various possibilities available, easily discernible in the spoken language because of the intonation cues, make out for a certain difficulty in the written part of the language, hence this unease at the reading of "only" in the OP's first sentence.

If "as" could be in the wrong position it has to be in the second sentence; however, I would not make such a strong assertion: there is not doubt that "as" expresses cause in the position it occupies in the second sentence, it's just that it seems to be not as effective as the "as" in the first sentence, whatever the reason; I suspect that this is so because it could be used often in that position as the conjunction relative to time. Both sentences are acceptable but the addition of the precision "instead of studying" in the first one removes any doubt, would there be any.