You are right, in the standard formulation of TIMES, there are some discrepancies between the detailed accounting of the investment and fixed costs in the objective function and the assumed constant activities and average available capacities within each period. However, you can eliminate these discrepancies by using the switch $SET OBLONG YES (when using the standard objective formulation), or by using one of the alternative objective formulations (e.g. $SET OBJ MOD, $SET OBJ LIN).
Long answer:
Even though the designers of TIMES were highly qualified scholars and from prestigious universities, such as KU Leuven and McGill, there are indeed some discrepancies in the assumptions on the capacity evolution in standard TIMES. However, these discrepancies are not between the assumed activities and available capacities within periods, but between the detailed accounting of the investment and fixed costs in the objective function and the assumed more simplified evolution of the activities and capacities within each period, when period lengths are longer than one year.
There is also an alternative formulation available in TIMES, which assumes a linear evolution of activities and capacities between milestone years. That is another way of achieving the desired simplification of the model when using period lengths longer than 1 year.
Notwithstanding, in the objective function the evolution of capacities is always considered on a detailed year-to-year basis. Since many years now, the ETSAP community has been well aware of the small discrepancies between the objective function and the more simplified "physical" assumptions in the model. I will not try presenting any formal treatment of these discrepancies here, but their impacts can be easily analyzed and illustrated by simple test models. For the specific case mentioned (investment Case 1.a), see the illustrative analysis in the following note:
In summary, to some extent such discrepancies exist in the standard formulation of TIMES, but their impacts are usually quite small, typically at most a few per-cent of the marginal costs. Moreover, in order to eliminate the impacts of the discrepancies, you can use the switch $SET OBLONG YES (for the standard objective formulation), or one of the alternative objective formulations (e.g. $SET OBJ LIN, $SET OBJ MOD). I would recommend using some of these options when concerned.