Artifically increasing the reputation level grants the robot a level of moderation it simply did not earn. The users providing reputation may have earned it, but the bot did not, therefore the community has no reason to trust it with moderation powers.
However, we need to find a way to resolve this question because the rate of spam and abuse is increasing, and human moderation is linear, so we should enable users to make bots that have some ability or power - but they should also be held accountable for bots they deploy.
History of reputation
Reputation was originally intended to track closely with a person's ability to help others, through question and answer upvotes, and was designed from the start to provide opportunities to moderate content on the site as one gained reputation.
Eventually it was extended to other useful operations on the site, such as editing, but only in a very limited manner. Other desirable objectives are awarded using badges primarily to avoid turning reputation into a payment system of some sort.
When bounties were added they were very vigorously debated and ultimately designed to limit abuse so that reputation still largely represented a person's ability - and as they are currently used bounties aren't altering this because users typically only apply bounties to hard problems, and the users that answer these problems well are obviously deserving of their reputation.
Robot hasn't earned community's trust
All this leads to the conclusion that a robot, by the site's definition, that can't ask and answer questions without human aid, nor edit without human aid, cannot earn reputation.
If anything, reputation can only be given it - undeservedly so.
We don't award reputation for flagging. If that is the only value the robot has, then there is no way it could or should earn reputation.
Possible courses of action
As such I don't believe this is a valid course of action. If a robot is provably useful, then questions here on Meta should be used to bring up the usefulness and whether it can or should be integrated into stack overflow's code base.
Alternately, it may be worthwhile to take the tack of an existing robot - the community user. Stack Overflow may be willing to provide accounts with certain restricted abilities - and they may choose the easy way by providing reputation - or they may have hidden fields and flags that allow this for reputationless users. Regardless, this should still occur outside the normal reputation system, and the bot should not be treated as a user of any kind.
A third option is to convince the community of the utility of flagging, and provide reputation for flagging. In the past such proposals have failed, but if the level of spam is such that this is useful now, then it may be that it's worth revisiting. This will, however, have to allow users with 1 reputation to flag so a bot may then earn reputation doing what it can. Perhaps 1 rep for a good flag and -10 rep for a rejected flag, for instance.
At this point the bot should be guiding users to act, as it is currently doing, but automating actions should not be provided to the bot until it reaches the needed reputation level without human interference on its own.
Artificially increasing the reputation level grants the robot a level of moderation it simply did not earn. The users providing reputation may have earned it, but the bot did not, therefore the community has no reason to trust it with moderation powers.