OP Doubt is valid , though easily resolved.
(1) Why Current Definition is enough :
$3.6.1$ talks about two sets having the Same Cardinality , without assigning a Natural number to that Cardinality.
Hence $X=Y=\phi$ will have the same Cardinality , which is as yet unknown.
OP is right that there is no Bijection between $\phi$ & every other set , hence $X=\phi$ & $Y \ne \phi$ will not have the Same Cardinality.
We can still claim that $X=\phi$ & $Y=\phi$ have the Same Cardinality.
[[ We have one trivial vacuous Bijection involving $\phi$ , Elaborate Discussion about this at the end ]]
$3.6.5$ assigns Cardinality $n$ when we have $1 \le i \le n$
Eg , we assign $n=1$ to $\{A\}$ & we assign $n=4$ to $\{A,B,C,D\}$
When we have $n=0$ , then $1 \le i \le n$ indicates $1 \le i \le 0$ , which is $1 \le 0$ , which is obviously the empty list. Hence $X=\phi$ works here.
Tao could have been a bit more explicit about this Case , though there is no major concern here.
(2) When we "Demand" that Current Definition is not enough :
Alternatively , let us say the Definitions are really not enough.
It is easy to add $3.6.0$ which "hardcodes" the Empty Set with Cardinality $0$.
(3) Why Current Definition is useful :
We want to make theorems about $\#(A \cup B)$ & $\#(A \cap B)$ (& more !) with $\#A$ & $\#B$ : Then those theorems should work even when $\phi$ occurs.
Hence we can not go with OP claim/thinking that "Cardinality of Empty Set is not defined" : All calculations should involve Natural numbers , with no Exceptions , within the finite Context.
Assigning $0$ to Empty Set makes us add & subtract $0$ where necessary.
Considering it undefined will make things more complicated later.
(4) What is the trivial vacuous Bijection involving $\phi$ :
There is no Bijection between $X=\{A,B,C\}$ & $Y=\{1,2,3,4\}$ , because we will consume all elements of $X$ while $Y$ will have 1 element left over.
There is no Bijection between $X=\{A,B,C,D\}$ & $Y=\{1,2,3\}$ , because $X$ will have 1 element with no matching element in $Y$.
When we have $X=\{A,B,C,D\}$ & $Y=\{1,2,3,4\}$ , then we can map $A$ to either of the 4 elements.
Then we can map $B$ to either of the 3 elements.
Then we can map $C$ to either of the 2 elements.
$D$ will map to the last element.
Hence we have $4!$ Bijections.
In general we have $n!$ Bijections.
Here is one way we can get the Bijection & reduce the number of elements in $X$ & $Y$ , until we get the Null Set :
$\#X=\#Y=4$ : $\{(A,3),(C,1),(B,2),(D,4)\}$ : $4!=24$ Possible Bijections
$\#X=\#Y=3$ : $\{(A,3),(C,1),(B,2)\}$ : $3!=6$ Possible Bijections
$\#X=\#Y=2$ : $\{(A,1),(B,2)\}$ : $2!=2$ Possible Bijections
$\#X=\#Y=1$ : $\{(A,1)\}$ : $1!=1$ Possible Bijection
$\#X=\#Y=0$ : $\{\}$ : $0!=1$ Possible Bijection
We can see that Empty Set has Exactly 1 trivial vacuous Bijection.
We have used all elements of $X$ , while no element of $Y$ is left over !
Hence $\phi$ has a Proper Bijection !