Encrypting a string as smaller pieces vs. encrypting it as a whole Is there any difference between these two ways to encrypt a string using FPE?

Say the string has the format is specified by this rule
First part is in the set 
$S = \{\text{AA,AB,AC,BA,BB,BC,CA,CB,CC}\} = \{0,1,2,3,4,5,6,7,8,9\}$, 
second part is in the set 
$T = \{0,1,2,3,4\} = \{0,1,2,3,4\}$

Example string = $\text{BA2}$

Usage 1.
Break the string as parts defined above, determine the integer representing each part as defined by the bijective mapping, and encrypt those integers individually using encryption function $E$.

$\text{BA = 3}$

$2 = 2$

$E(3) \Rightarrow 6 = \text{CA}$

$E(2) \Rightarrow 4 = 4$

Concatenate the parts together to get output 

Output string = $\text{CA4}$

Usage 2
Encrypt the entire string by ranking all possible values.

$S=\{\text{AA0, AA1, AA2, AA3, AA4, AB0, AB1 ,AB2 ,AB3, AB4, AC0, AC1, AC2, AC3, AC4,}$ $\text{BA0, BA1, BA2, BA3, BA4, BB0, BB1, BB2, BB3, BB4, BC0, BC1, BC2, BC3, BC4,}$
$\text{CA0, CA1, CA2, CA3, CA4, CB0, CB1, CB2, CB3, CB4, CC0, CC1, CC2, CC3, CC4}\} = \{0,1,2,3...43,44\} $

$E(17) \Rightarrow 8 $

Output string  = $\text{AB3}$

Is Usage 1 equally valid as Usage 2?  Are there any negative side effects to breaking the string into pieces first compared to encrypting the string as a whole?
(1) correct a mistake here:


  set S = {AA,AB,AC,BA,BB,BC,CA,CB,CC} = {0,1,2,3,4,5,6,7,8,9}


should be 
set S = {AA,AB,AC,BA,BB,BC,CA,CB,CC} = {0,1,2,3,4,5,6,7,8}

(2) According to your example. I would say the "Usage 2" is better than the "Usage 1", since the "Usage 2" has more possible mappings than the "Usage 1" does. 
Proof:
Usage 1: 
1. E function works for both set S (size = 9) and set T (size = 5).
2. When E function's input is in the {0,1,2,3,4}, its output must also be in the {0,1,2,3,4}. Or, you cannot map "the set T = {0,1,2,3,4} = {0,1,2,3,4}" by the E function.
3. This leads to a problem: the first 5 elements in S ("AA,AB,AC,BA,BB") can only be mapped to a subset of S ("AA,AB,AC,BA,BB"). For example, you will never map "AA0" to "BCX", "CAX", "CBX" or "CCX", where X is in the {0,1,2,3,4}.

"Usage 2": 
All possible mappings are here.

(3) According to your two comments:


  @D.W.the string is only 3 bytes composed of characters only from the sets above. The output scope should be the same as the input - the function E puts you back into the same set from which the value came from – erotavlas 8 hours ago 
  
  In Usage 1, I could encrypt them as separate entities (pass them to an integer FPE with different max value for each) – erotavlas 8 hours ago 


I would also say that the "Usage 2" is better than the "Usage 1".
Proof:
A1. the E function now maps S(9) to S(9), T(5) to T(5), S'(45) to S'(45), where S' is the S of your Usage 2 example;
A2. "Usage 1": I will feed your E function 9 inputs to get all possible mappings(S=>S, T=>T). That is, {AA0, AB1, AC2, BA3, BB4, BCx, CAx, CBx, CBx}, where x is a number in the T set.
A3. "Usage 2": I will feed your E function 45 inputs to get all possible mappings(S'=>S'). That is, the whole S' set as specified in A1.
A4. The difference is that by dividing the string into small pieces, the spaces of clear text and cipher text are changed.