Method overloading resolution has three stages. The first and second stages don't consider methods with varargs (also called variable arity methods) as candidates, so only if no matching method without varargs is found, the compiler considers method with varargs as candidates.
Therefore, in the first and second method calls, your void method(int ... a) is ignored, and there is no ambiguity.
15.12.2. Compile-Time Step 2: Determine Method Signature
The second step searches the type determined in the previous step for
member methods. This step uses the name of the method and the argument
expressions to locate methods that are both accessible and applicable,
that is, declarations that can be correctly invoked on the given
arguments.
There may be more than one such method, in which case the most
specific one is chosen. The descriptor (signature plus return type) of
the most specific method is the one used at run time to perform the
method dispatch.
A method is applicable if it is applicable by one of strict invocation
(§15.12.2.2), loose invocation (§15.12.2.3), or variable arity
invocation (§15.12.2.4).
Certain argument expressions that contain implicitly typed lambda
expressions (§15.27.1) or inexact method references (§15.13.1) are
ignored by the applicability tests, because their meaning cannot be
determined until a target type is selected.
Although the method invocation may be a poly expression, only its
argument expressions - not the invocation's target type - influence
the selection of applicable methods.
The process of determining applicability begins by determining the
potentially applicable methods (§15.12.2.1).
The remainder of the process is split into three phases, to ensure
compatibility with versions of the Java programming language prior to
Java SE 5.0. The phases are:
The first phase (§15.12.2.2) performs overload resolution without permitting boxing or unboxing conversion, or the use of variable arity
method invocation. If no applicable method is found during this phase
then processing continues to the second phase.
This guarantees that any calls that were valid in the Java programming language before Java SE 5.0 are not considered ambiguous
as the result of the introduction of variable arity methods, implicit
boxing and/or unboxing. However, the declaration of a variable arity
method (§8.4.1) can change the method chosen for a given method method
invocation expression, because a variable arity method is treated as a
fixed arity method in the first phase. For example, declaring
m(Object...) in a class which already declares m(Object) causes
m(Object) to no longer be chosen for some invocation expressions (such
as m(null)), as m(Object[]) is more specific.
The second phase (§15.12.2.3) performs overload resolution while allowing boxing and unboxing, but still precludes the use of variable
arity method invocation. If no applicable method is found during this
phase then processing continues to the third phase.
This ensures that a method is never chosen through variable arity method invocation if it is applicable through fixed arity method
invocation.
The third phase (§15.12.2.4) allows overloading to be combined with variable arity methods, boxing, and unboxing.