fix(check): align skipLibCheck default with tsgo

[bartlomieju]

Deno's base check compiler options defaulted skipLibCheck to false, while
the generated tsconfig used by native deno check defaulted it to true. That
split meant the two halves of the check pipeline disagreed on whether .d.ts
files are type-checked, and it also made the native check-hash collide across
runs that used different effective skipLibCheck values (a clean run under the
implicit false default would satisfy a later run that should have checked lib
files, and vice versa).

This flips the resolved base default to true so the whole pipeline (native
check, the in-isolate check path shared by deno run --check/test/cache,
and the LSP) agrees on tsgo's --init default of skipLibCheck: true. A user
skipLibCheck: false still overrides it, and that override is now sourced from
the resolved compiler options (which honor --config <other>) rather than the
raw project-root deno.json pass, so it is respected however the config is
provided.

With the default settled, this re-enables the .d.ts entrypoint check specs
that were ignored under #36085: under the aligned default a .d.ts entrypoint
(or a referenced .d.ts dependency) is not type-checked, and each spec now also
covers the skipLibCheck: false path that does surface the error. The specs run
in per-test temp dirs so their generated .deno/ and check caches don't clobber
one another.

Closes #36085