Definition of Random Variable: Suppose $(\Omega,\Sigma,\mathbb P)$ is a probability space. If $\mathbf Y : \Omega \mapsto \mathbb R$ is measurable w.r.t. the Borel $\sigma$-algebra on $\mathbb R$, then $\mathbf Y$ is called a Random Variable. The $\sigma$-algebra generated by $\mathbf Y$ is: $\sigma(\mathbf Y)=\{ \mathbf Y^{-1}(A):A\in\mathscr B(\mathbb R)\}\subset\Sigma.$
Definition of Independent Random Variables: Two random variables $\mathbf X$, $\mathbf Y$ are independent if events A and B are independent (i.e. $\mathbb P(A\cap B)=\mathbb P(A)\mathbb P(B)$), whenever $A\in\sigma(\mathbf X)$ and $B\in\sigma(\mathbf Y)$.
Question 1: Why do we only consider $\mathscr B(\mathbb R)$ here? The measurable collection of set on $\mathbb R$ could be extended beyond the Borel sets if we give a measure (e.g. Lebesgue measure). Although the extension is to include null-sets, we get a lot more sets (by intersection/union of null-sets with Borel sets), why do we do not require $\mathbf Y$ to be measurable over them as well? Plus, even if N is a null-set on $(\mathbb R,\mathscr A,\mu)$, it does not mean $\mathbf Y^{-1}(N)$ is a null-set on $(\Omega,\Sigma,\mathbb P)$ - it could has a positive probability, and thus is not boring/trivial.
Question 2: When it comes to independence of $\mathbf X$ and $\mathbf Y$, why do we only consider events in $\sigma(\mathbf X)$ and $\sigma(\mathbf Y)$? Why do we not care about events such as $L\in(\Sigma\setminus\sigma(\mathbf X))$ and $M\in(\Sigma\setminus\sigma(\mathbf Y))$? (i.e. $\mathbb P(L\cap M)\neq\mathbb P(L)\mathbb P(M)$ does not affect the independence of $\mathbf X$ and $\mathbf Y$). Note that for $L\in(\Sigma\setminus\sigma(\mathbf X))$ and $M\in(\Sigma\setminus\sigma(\mathbf Y))$ with $\mathbb P(L\cap M)\neq\mathbb P(L)\mathbb P(M)$, although $L\notin\sigma(\mathbf X)$, it is still somehow relevant to $\mathbf X$, because $\mathbf X$ is defined on every point of the set L, and maps those points to $\mathbb R$. For example, there could be set $P\in\sigma(\mathbf X)$ and $P\cap L\neq\emptyset$, so X could be defined on some points of $L$ despite of the fact that $L\notin\sigma(\mathbf{X})$.
UPDATE: summarize answers + my thoughts
Big thanks for both answers, very helpful!
For Question 1: To summarize the answers: examples were given about a mapping between probability space (which is e.g. $(\mathbb R,\mathscr M,\mathcal{L})$) to $\mathbb R$. And that mapping will map a $\mathcal{L}$-measurable set inversely back to a non-$\mathcal{L}$-measurable set in probability space. For example (from Halmos's Measure theory §19. Problem 3.) let f(x) = 0.5*(x + c(x)), where c(.) is a Cantor function. And then let $C$ be the Cantor set, $\exists A \subset C$ s.t. $A$ is $\mathcal L$-measurable but not a Borel set, and $F^{-1}(A)$ is not $\mathcal L$-measurable (Refer to this post). Extended discussion: the above issue could be solved by two ways: 1) we give up Lebesgue sets but go with Borel sets (which is exactly our definition); but we could also do 2) Maintain Lebesgue sets, but give up those mappings as a valid random variable. In terms of why is it important to keep functions like above (i.e. maps Lebesgue measurable sets inversely back to a non-measurable set) to be a random variable, and thus we eventually choose 1) over 2)? - Please see @zoli's comments below
For Question 2: To summarize the answers: The parity example by @zhoraster is a good one, for illustrating "independence meaning probability able to multiply" v.s. "normal meaning of generally not dependent"), but this is NOT the issue confusing me. What really bothers is that the property (independence) of v.r. is defined based on $\mathit subsets$ of $\Omega$; yet v.r. itself based on $\mathit elements$ of $\Omega$. @zoli mentions wiki does give definition of independence with intervals and cdf, but per @Did's comment, and I also personally feel that, independence itself does not necessarily need to rely on those concepts - instead, could be just by the independence of $\sigma$-algebra generated by the r.v. Extended discussion: I think @zoli's comment could be close, that "Events not belonging to the $\sigma$−algebra generated by a random variable cannot be described using only statements about the random variable." - My own thoughts on this: although we define $\mathbb P$ over $\Omega$ for all elements in $\Sigma$, what could really be carry through the r.v. $\mathbf X$ is $\mathbb P_X(A)=\mathbb P(\{\omega|\mathbf X(\omega)\in A\})$, where $A\in\mathscr{B}(\mathbb R)$, thus set $L$ or $M$ above might have a measure under $\mathbb P$, we cannot reflect that via $\mathbb{P}_X$ or $\mathbb{P}_Y$. Further, if we do care about those events, we'll pick a r.v. $\mathbf Z$ s.t. $L\in\sigma(\mathbf Z)$. BTW, from wiki: "the underlying probability space $\Omega$ is a technical device...In practice, one often...just puts a measure on ${\mathbb {R} }$...".