All we have right now in measurable metrics is the number of guilds at 95-100 and their guild size. If the number of large guilds at 95-100 outnumber the small guilds at 95-100 then the current size bonus will need to be re-evaluated and boosted up.
If with this change increases the number of large guilds at 95-100 over that of the current small guilds at 95-100. That should prove that large guilds are the only ones benefiting from this change. If large guilds are rapidly hitting the 3 level cap after this change, per the concern, that can be measured and addressed. Should large guilds not be affected outside of a slow progression to next level, this also can be measured. If small guilds under a certain size is not progressing in the manner of the guild the next tier up, that can be monitored and addressed.