1. It's unlikely that you would be considered non UK resident based on those facts. Firstly, if you average more than 91 days in the UK over a 4 year period, you won't be non UK resident. Secondly, even if you get below that limit, you need to show that you have left the UK. This is a much more subtle test, but it does not help your case if you have a house in the UK. You don't mention if you are married - but if you are and your wife is staying in the UK, that would be another factor against you being non UK resident.
Is HMRC more relaxed in smaller cases? Not really. They may well try to target larger cases, but they don't really know how big a case is until they have picked it. Once they have picked you, you can expect them to pursue the matter doggedly even if the costs they run up bear no relation to the tax at stake.
2. Yes, rental income from UK property would be taxable in much the same way if you were non UK resident. Likewise, personal pensions would be taxable.
3. If you were non UK resident, you would not be liable to CGT on your house unless you returned within 5 years, so PPR would not be an issue. You are right to say the last 3 years qualify for PPR in any event.