I am a university faculty supported by this Simons Foundation research grant. Who decides on the spending rules for this grant? Can my universty impose any rules, for example acomodation cost limits or a requirement that any use of funds requires a justification as to how it "benefits" my university?
Generally speaking, with possible exceptions, spending rules are decided by the funding agencies, but universities may impose additional constraints within the rules set by the agencies.
For instance, I participate to several European projects funded by a certain agency. When travelling, participants to the same project from different institutions have different travel and subsistence limits, and these are set by the institutions. The differences in these limits across the institutions can be fairly large, and the limits may be even different within the same institution depending on the rank of the people travelling.
Furthermore, yes, any use of the funds within a certain grant typically needs to be justified. For instance, if I travel to a conference and I want the travelling expenses to be covered by that grant, I'm required to submit at least a paper acknowledging the grant.
When buying instruments, the institution can set the rules according to which an instrument can be bought and in which way its operating time within the project should be recorded.
Some institutions might have relaxed constraints with respect to others, but generally don't expect to be able to freely dispose of your grant money without justification. And the funding agencies may send revisers years later to verify that the grants had been used according to the rules.
As @Massimo_Ortolano remarks, universities frequently impose constraints on how grant funds may be spent that are over and above the constraints imposed by the granting agency.
That said, the constraints imposed by the Simons Collaboration itself are in fact detailed on the very page to which you provided a link. There are within-page links, one detailing the things on which funds are permitted to be spend (Allowable Expenses) and the other, explaining what should happen to unspent funds at the end of the grant period.
The information headings (i.e., "allowable expenditure" and "unspent") funds are fairly typical of many granting agencies. More specifically, if you locate the website for a granting agency, then you might be able to search from within the agency itself for those headings, or alternatively use Google with a search such as:
site:thegrantingagency.gov "unspent funds" OR "allowable expenses" OR "allowable expenditure"