While it is true that one is much larger than the other in that we have $G_{\operatorname{TREE}(3)}-\operatorname{TREE}(3)$ being large, a linear scaling such as this is not very useful for comparing large numbers.
A simpler analogy would be $10^{1,000,000,000,001}$ and $10^{1,000,000,000,000}$. Although we have their difference being as big as $9\times10^{1,000,000,000,000}$, it probably does not seem like one is "significantly" bigger than the other.
One way to clarify what is meant here is by considering how the numbers are constructed, rather than the numbers themselves. When viewed from this perspective, it is clear to see that $10^{1,000,000,000,001}$ and $10^{1,000,000,000,000}$ are "made" the same way.
On the other hand, something such as $10^{10^{10^{10}}}$ is significantly larger than $10^{1,000,000,000,000}$ because it uses repeated exponentiation, which is far larger than just exponentiation.
In the same way, one could argue that
$$^{1,000,000,000,001}10=10^{10^{10^{.^{.^.}}}}\bigg\}1,000,000,000,001\text{ powers of }10$$
is not significantly larger than
$$^{1,000,000,000,000}10=10^{10^{10^{.^{.^.}}}}\bigg\}1,000,000,000,000\text{ powers of }10$$
Going back to our first example, one number was simply $10$ times larger than the other. In general, after a certain point, multiplying by $10$ is not significant. After a certain point, exponentiating one more time is not significant either. After a certain point, $G_n$ is not significantly larger than $n$.
To be more precise about how far one has to go for something to be considered insignificantly larger, we used in our examples:
$f(n)$ is not significantly larger than $n$ when $n\ge\underbrace{f(f(f(\dots f(}_{1,000,000,000,000}k)\dots)))$, for fast growing functions $f$ and some sufficiently large $k$, say $k=10$.
This is, of course, very informal. Another way we could try to formulate this is with the fast growing hierarchy, as Peter mentioned, which can be made more formally.