For the main battery there will probably be no problem using generic NiMH cells in place of the originals.
Treatment of main and backup/RTC batteries may vary somewhat.
The main battery can probably be replaced with off the shelf NiMH AA alternatives. Charge termination is usually by negative delta V or temperature rate increase or absolute temperature and say 3000 mAh cells should be close enough to the 2600 mAh cells to work similarly.
Paradoxically, the lower capacity RTC and standby batteries may be more complex to deal with.
Presumably the RTC and backup charging circuitry depends on limiting maximum voltage of the batteries, rather than any of the methods usually used for higher power applications.
Presumably the existing RTC and backup chargers are designed to not destroy the originally specified cells.
Replacements with higher capacity MAY be subject to charging runaway.
NiMH charging voltage at low rates (< C/10) should be no more than about 1.4 V/cell. It is possible that an even lower voltage than this may be appropriate if the charge rate is very low.
So if eg the 7.2V battery is 7.2/1.2 = 6 cells, the maximum charging voltage should be <= 1.4 x 6 = 8.4 V. Much more than this and you risk "runaway" with the battery charging indefinitely. Actual Vmax is dependant on charge rate, battery capacity and to some extent brand and model. (Ask me how I know :-) ).
Historically NiMH AA cells under about 1800 mAh could be trickle charged at < C/10 indefinitely. These cells contained chemical and internal structure which chemically recombined H2 and O2 generated by electrolysis when the cell was fully charged. As cell capacities increased the recombination systems were removed to make more room for active ingredients. NiMH AA cells over above 2000 mAh capacity MUST NOT be trickle charged. "Trickling" results in gas generation, leading to venting which causes loss of electrolyte and rapid cell failure.
How this relates to the very low capacity RTC and standby cells depends on the charging circuitry and c ell construction.
Who would have thought it could be so uncertain? :-).