To answer your question, the case you are referring to is Hussainara Kharoon v. State of Bihar, 1979 AIR 1369, 1979 SCR (3) 532, which has laid down that anybody who is in prison for a time exceeding the maximum imprisonment that they could’ve been given for the crime committed by them should be immediately set free. Now as you have already mentioned this has essentially been given cognizance in Section 436 (A) Cr.P.C.
The judgement in the case is essentially a reiteration of the same principle given for added emphasis. Added to that is the fact that the pronouncement is a stringent one and revolutionary of sorts as far as rights of under trials are concerned. Such judicial pronouncements tend to catch the eye of the media and due to the enhanced media coverage that they receive this information gets disseminated to the general public who is thus more aware of their rights. This thus helps raise general awareness about such rights and hence is a positive step to be included in the judgement.
As far as the question of bail is concerned, the amount of bail set is not dependent on the ability of the person to pay, but on the grievousness of the offence committed, or whether there is a threat of him skipping town and not showing up for further proceedings. A major factor in determining the amount of bail in a current matter is the character and former criminal record of the defendant. It has been held, however, that the criminal activities and tendencies of a person applying for bail on a charge of vagrancy do not justify the fixing of bail at an excessive amount for the purpose of keeping him in jail. It has time and again been said that a court should give some regard to the prisoner's pecuniary circumstances, since what is reasonable bail to a man of wealth may be equivalent to a denial of the right to bail if exacted of a poor man charged with a like offense (McCoy v United States, 123 App DC 81, 357 F2d 272; Beddow v State, 259 Ala 651, 68 So 2d 503; People ex rel. Sammons v Snow, 340 III 464, 173 NE 8, 72 ALR 798; Green v Peit, 222 Ind 467, 54 NE2d 281; State v Mastrial, 266 Minn 58, 122 NW2d 621, certden 375 US 942, 11 L Ed 2d 274, 84 S Ct 349; Royalty v State (Miss) 235 So 2d 718; Ex parte Royalty v State (Miss) 235 So 2d 718; Ex parte Malley, 50 Nev 248, 256 P 512, 53 ALR 395.) ( REFERENCE - http://www.legalserviceindia.com/articles/bail_poor.htm)
What needs to be kept in mind, however, is that bail is not rendered excessive only because the accused is unable to afford the amount. The monetary situation of the accused could be a consideration but it is no way legally required that the bail amount be set in such a way that the accused is able to afford it completely.
Thus you can say that in a way the bail system is in fact prejudiced against the poor. However, there is no denying the fact that it is of utmost importance to the legal system to make sure that the criminals are not let off easily and that they do attend the entire length of the proceedings instead of just absconding.
Coming to the point of protecting people against false cases, the fact is that such a practice is prevalent in India as a method of revenge but there are no legal safeguards as such apart from going through the trial process and proving your innocence in a court of law. The rationale behind the same is that these offences are too grave and the society just cannot afford to let these criminals get away. It is thus in the best interest of the society as a whole that such crimes are treated with utmost seriousness.