Summation under Zeckendorf Representation
APL (Dyalog Extended), 39 bytes



⊥1↓⍧|/⌽(+/g[⍸⌽+/⊤⎕]),↑,\⌽g←(2+/,)⍣38⍨⍳2


Try it online!

Changed into a full program taking one argument of length 2, and also changed the Fibonacci generator. Thanks to @ngn for lots of ideas.

Uses ⎕IO←0 so that ⍳2 evaluates to 0 1.

Fibonacci generator (new)

Note that the last two numbers are inaccurate, but it doesn't change the output of the program.

(2+/,)⍣38⍨⍳2
→ 0 1 ((2+/,)⍣38) 0 1

Step 1
0 1 (2+/,) 0 1
→ 2+/ 0 1 0 1
→ (0+1) (1+0) (0+1) ⍝ 2+/ evaluates sums for moving window of length 2
→ 1 1 1

Step 2
0 1 (2+/,) 1 1 1
→ 2+/ 0 1 1 1 1
→ 1 2 2 2

Step 3
0 1 (2+/,) 1 2 2 2
→ 2+/ 0 1 1 2 2 2
→ 1 2 3 4 4


Zeckendorf to plain (partial)

⍸⌽+/⊤⎕
     ⎕  ⍝ Take input from stdin, must be an array of 2 numbers
    ⊤   ⍝ Convert each number to base 2; each number is mapped to a column
  +/    ⍝ Sum in row direction; add up the counts at each digit position
 ⌽      ⍝ Reverse
⍸       ⍝ Convert each number n at index i to n copies of i




APL (Dyalog Extended), 47 bytes



g←1↓(1,+\⍤,)⍣20⍨1
{⊥1↓⍧|/⌽⍵,↑,\⌽g}+⍥{+/g[⍸⌽⊤⍵]}


Try it online!

Changed Part 1 of the previous answer to reuse the Fibonacci numbers. Also, drop the duplicate 1 to save some bytes in other places.

Part 1 (new)

{+/g[⍸⌽⊤⍵]}
       ⊤⍵    ⍝ Argument to binary digits
     ⍸⌽      ⍝ Reverse and convert to indices of ones
   g[    ]   ⍝ Index into the Fibonacci array of 1,2,3,5,...
 +/          ⍝ Sum




APL (Dyalog Extended), 52 bytes



{⊥1↓¯1↓⍧|/⌽⍵,↑,\⌽(1,+\⍤,)⍣20⍨1}+⍥({+∘÷⍣(⌽⍳≢⊤⍵)⍨1}⊥⊤)


Try it online!

How it works

No fancy algorithm to do addition in Zeckendorf because APL isn't known for operation on individual elements in an array. Instead, I went ahead to convert the two inputs from Zeckendorf to plain integers, add them, and convert it back.

Part 1: Zeckendorf to plain integer

{+∘÷⍣(⌽⍳≢⊤⍵)⍨1}⊥⊤  ⍝ Zeckendorf to plain integer
                ⊤  ⍝ Convert the input to array of binary digits (X)
{    (  ≢⊤⍵)  }    ⍝ Take the length L of the binary digits and
      ⌽⍳           ⍝   generate 1,2..L backwards, so L..2,1
{+∘÷⍣(     )⍨1}    ⍝ Apply "Inverse and add 1" L..2,1 times to 1
                   ⍝ The result looks like ..8÷5 5÷3 3÷2 2 (Y)
               ⊥   ⍝ Mixed base conversion of X into base Y

Base |             Digit value
-------------------------------
13÷8 | (8÷5)×(5÷3)×(3÷2)×2 = 8
 8÷5 |       (5÷3)×(3÷2)×2 = 5
 5÷3 |             (3÷2)×2 = 3
 3÷2 |                   2 = 2
 2÷1 |                   1 = 1


Part 2: Add two plain integers

+⍥z2i  ⍝ Given left and right arguments,
       ⍝   apply z2i to each of them and add the two


Part 3: Convert the sum back to Zeckendorf

"You may assume that the Zeckendorf representations of both input and output fit into 31 bits" was pretty handy.

{⊥1↓¯1↓⍧|/⌽⍵,↑,\⌽(1,+\⍤,)⍣20⍨1}  ⍝ Convert plain integer N to Zeckendorf
                 (1,+\⍤,)⍣20⍨1   ⍝ First 41 Fibonacci numbers starting with two 1's
                ⌽                ⍝ Reverse
             ↑,\                 ⍝ Matrix of prefixes, filling empty spaces with 0's
          ⌽⍵,                    ⍝ Prepend N to each row and reverse horizontally
        |/                       ⍝ Reduce by | (residue) on each row (see below)
       ⍧                         ⍝ Nub sieve; 1 at first appearance of each number, 0 otherwise
  1↓¯1↓                          ⍝ Remove first and last item
 ⊥                               ⍝ Convert from binary digits to integer


The Fibonacci generator

(1,+\⍤,)⍣20⍨1
→ 1 ((1,+\⍤,)⍣20) 1  ⍝ Expand ⍨
→ Apply 1 (1,+\⍤,) x 20 times to 1

First iteration
1(1,+\⍤,)1
→ 1,+\1,1  ⍝ Expand the train
→ 1,1 2    ⍝ +\ is cumulative sum
→ 1 1 2    ⍝ First three Fibonacci numbers

Second iteration
1(1,+\⍤,)1 1 2
→ 1,+\1,1 1 2  ⍝ Expand the train
→ 1 1 2 3 5    ⍝ First five Fibonacci numbers

⍣20  ⍝ ... Repeat 20 times


This follows from the property of Fibonacci numbers: if Fibonacci is defined as

$$
F_0 = F_1 = 1; \forall n \ge 0, F_{n+2} = F_{n+1} + F_n
$$

then

$$
\forall n \ge 0, \sum_{i=0}^{n} F_i = F_{n+2} - 1
$$

So cumulative sum of \$ 1,F_0, \cdots, F_n \$ (Fibonacci array prepended with a 1) becomes \$ F_1, \cdots, F_{n+2} \$. Then I prepend a 1 again to get the usual Fibonacci array starting with index 0.

Fibonacci to Zeckendorf digits

Input: 7, Fibonacci: 1 1 2 3 5 8 13

Matrix
0 0 0 0 0 0 13 7
0 0 0 0 0 8 13 7
0 0 0 0 5 8 13 7
0 0 0 3 5 8 13 7
0 0 2 3 5 8 13 7
0 1 2 3 5 8 13 7
1 1 2 3 5 8 13 7

Reduction by residue (|/)
- Right side always binds first.
- x|y is equivalent to y%x in other languages.
- 0|y is defined as y, so leading zeros are ignored.
- So we're effectively doing cumulative scan from the right.
0 0 0 0 0 0 13 7 → 13|7 = 7
0 0 0 0 0 8 13 7 →  8|7 = 7
0 0 0 0 5 8 13 7 →  5|7 = 2
0 0 0 3 5 8 13 7 →  3|2 = 2
0 0 2 3 5 8 13 7 →  2|2 = 0
0 1 2 3 5 8 13 7 →  1|0 = 0
1 1 2 3 5 8 13 7 →  1|0 = 0
Result: 7 7 2 2 0 0 0

Nub sieve (⍧): 1 0 1 0 1 0 0
1's in the middle are produced when divisor ≤ dividend
(so it contributes to a Zeckendorf digit).
But the first 1 and last 0 are meaningless.

Drop first and last (1↓¯1↓): 0 1 0 1 0
Finally, we apply base 2 to integer (⊥) to match the output format.