Gurobi has apparently been listening to you and others with similar concerns. Gurobi 9.1 was just released and introduces a new parameter IntegralityFocus to somewhat ameliorate those concerns (although I haven't tried it yet, so don't know how well).
Gurobi 9.1 Reference Manual page for InetgralityFocus
Integrality focus
Type: int
Default value: 0
Minimum value: 0
Maximum value: 1
One unfortunate reality in MIP is that integer variables don't always
take exact integral values. While this typically doesn't create
significant problems, in some situations the side-effects can be quite
undesirable. The best-known example is probably a trickle flow, where
a continuous variable that is meant to be zero when an associated
binary variable is zero instead takes a non-trivial value. More
precisely, given a constraint $y \le M b$
where $y$ is a non-negative continuous
variable, $b$ is a binary variable, and
$M$ is a constant that captures the largest
possible value of $y$, the constraint is
intended to enforce the relationship that
$y$ must be zero if
$b$ is zero. With the default integer feasibility tolerance, the binary variable is allowed to take a value
as large as $1e-5$ while still being
considered as taking value zero. If the $M$ value is large, then the $M$ upper bound
on the $y$ variable can be substantial.
Reducing the value of the IntFeasTol parameter can mitigate the
effects of such trickle flows, but often at a significant cost, and
often with limited success. The IntegralityFocus parameter provides a
better alternative. Setting this parameter to 1 requests that the
solver work harder to try to avoid solutions that exploit integrality
tolerances. More precisely, the solver tries to find solutions that
are still (nearly) feasible if all integer variables are rounded to
exact integral values. We should say that the solver won't always
succeed in finding such solutions, and that this setting introduces a
modest performance penalty, but the setting will significantly reduce
the frequency and magnitude of such violations.