I prefer to return back to the original papers when trying to explain (or understand) an effect. If you were taking a class in the 1960's, you'd be taught the details. But modern teaching has so much else to cover and it usually sacrifices deeper approaches that include a physical understanding in the interests of getting on with the business of teaching the necessaries of practical models. Understanding it is left to the student per their own time and inclinations.
The paper you want to read is "Effects of Space-Charge Layer Widening in Junction Transistors" by J. M. Early. (Who is known to have disliked the name "Late Effect" -- later added to the Gummel-Poon BJT model.)
I'll borrow Figure 1 from his paper:
Here, Dr. Early is showing a simplified model of the NPN BJT. The base region thickness is labeled as \$W\$ and the collector's barrier thickness is labeled as \$X_{_\text{M}}\$. (The emitter barrier is usually forward-biased and it is so thin that it can be neglected in the diagram.)
If the reversed collector potential (relative to the base potential) is increased in magnitude, \$X_{_\text{M}}\$ also increases in thickness. But it doesn't go in just one direction, spreading outward into the collector region, as Dr. Shockley earlier assumed (and then used this incorrect assumption to mathematically prove that the collector current was independent of the collector reverse potential -- wrong.) Instead, \$X_{_\text{M}}\$ spreads in both directions (but not necessarily equally so.) The portion spreading into the base region has the effect of reducing thickness \$W\$.
This decrease in \$W\$ decreases the probabilities and therefore the rate of recombination of charges in the base layer as the collector current passes through the now-thinner base layer (charges spend less time transiting there.) This therefore increases the effective transport factor, \$\beta\$. (Note that we've since lost the use of that phrase, too.)
(This also leads to changes in the distributed, but usually lumped, impedances such as the base and emitter impedances. But that's not part of your question or the model you are currently exposed to.)
why don't we account for change in base current due to Vce changes in
small signal model?
The small-signal model you are being exposed to is based upon the non-linear, large-scale, hybrid-\$\pi\$, but applying calculus to derive from that a linearized small-signal model. This linearized version of that particular Ebers-Moll model (there are three completely equivalent models, as you can see at the link) is just the tangent line at some point along this "level 1" Ebers-Moll model.
The level 1 (and level 2, later) Ebers-Moll model was developed before the Early Effect was described and therefore does not include it. These earlier models were modified, in the level 3 version, to include a new parameter called the Early voltage as a way of accounting for how the width of the base is modulated by the base-collector reverse voltage magnitude:
(The above image comes from Ian Getreu's "Modeling the Bipolar Transistor." on page 45.)
Those slopes are relatively linear over a useful range and, because they relate voltage and current, can be seen as an added resistance to the small scale model.
However, they are not modeled in the BJT in that fashion in Spice. Nor should they be. That resistance is strictly a small signal equivalent and it only applies to the linearized small-signal model. The large-scale model that Spice must use does not include such a beast. Instead, when using the level 3 Ebers-Moll model (or Gummel-Poon) it modifies the forward transport factor \$\beta\$, the saturation current, and the forward transit time.