I advise based not only on the rules but the practical application of those rules based on large numbers of applications.
You are allowed to submit an application within 28 days of a visa expiring. The discussion comes down to what is considered to be the expiry date where an application was submitted 'in time' and the Home Office took their time to make a decision - in other words, the applicant's visa has expired, sometimes by quite a considerable amount of time, due to the time taken by the Home Office. The applicant should not be penalised for this and therefore it has been accepted for quite some time that if an application is returned to the applicant, invalid or refused, then the applicant will normally be allowed to quickly submit a new application. This is a key point.
I have known many applications like this and have not personally had any refused for this reason.
Right of appeal is usually determined simply by whether or not the applicant has valid leave to remain at the time of a refusal being issued (put in simple terms). You also need to be careful when drawing conclusions from other people's experiences - very often people are refused for reasons that are not exactly the reasons that they think they have been refused for. I'm not saying that this is the case in the examples you mention but it does happen, in the same way as people get approved and think they have done things right when in fact they simply got lucky.
Don't forget that for Long Residence the rules are a little bit more relaxed than for the 5-year qualifying period.
Again, if the application is put together well and the only issue is resubmission upon receipt of refused or invalid applications then I would not expect the application to be refused solely for this reason.
With regard to your last question, I think legal representation can be very useful for Long Residence applications.