I have a before-load user event script that pre set some customization, till now it was only used for creating new kit items will that not work if I'm editing the old record?

var record = context.newRecord;

In a user event script, oldRecord newRecord just refer to the state of a record before or after some chages have been made. On create, there is only newRecord, and on delete there is only oldRecord. Every other action has both. So, even though it is an old record (in the sense that it was created a while ago) it will still have context.newRecord, however, that will contain the changes being made, not the data originally there before the changes.

if the user is editing the record this should still work

var record = context.newRecord;

    record.setValue({ fieldId: "subsidiary", value: 2 });
    record.setValue({ fieldId: "taxschedule", value: "1" });
    record.setValue({ fieldId: "custitem_fa_amz_flag01", value: 1 });

yes, though if the user actually changed any of those fields, your script will overwrite those changes

this is a before load

okay, that will work differently then