How can I argue that $3\mathsf{SAT}\leq_p \mathsf{IndSet}$ is polynomial in time?
You are given a formula, and you will construct a graph. You can argue the reduction is polynomial time by analyzing the time you need to construct the graph. The transformation is an algorithm: write each step down, and analyze them. If every step takes polynomial time, you have shown the reduction runs in polynomial time.

Scan the clauses of the formula in time that is linear in the number of clauses. Scan the 3 literals in every clause. Build 3 vertices, with labels corresponding to the literals in a clause. This you can do in constant time, clearly. Once you have built a triangle, add it to your graph. With reasonable assumptions, you can do this in linear time, but details naturally depend on the way you represent your graph. Nevertheless, the time taken will be polynomial.

Finally, you only need to add edges between any two complementary literals from different triangles. Scan your triangles. For every literal in the triangle, scan through every other triangle, and see if there is a complementary triangle. If so, add an edge. This process takes polynomial time; for every triangle you are scanning every other triangle, so think of something quadratic. After every triangle has been scanned, $G_\phi$ has been built.