The first document you mentioned is actually a Standard Note (SN/HA/5524).
The Standard Note also states:
"However, statutory guidance states that compensation for such
damage is "unlikely to be appropriate if the search was lawful, and the force used can be shown to be reasonable, proportionate and necessary to effect entry.""
It also states:
"This information is provided to Members of Parliament in support of their parliamentary duties and is not intended to address the specific circumstances of any particular individual. It should not be relied upon as being up to date; the law or policies may have changed since it was last updated; and it should not be relied upon as legal or professional advice or as a substitute for it."
The second document you mention lays out procedures for City of London Police for forced entry. This would not apply to the Metropolitan Police Service.
The document also states:
"During high risk operations there is a real risk of officers and members of the public being injured, or property damaged. This policy, potentially, saves the force on cost of any speculative claims for compensation from suspects targeted on intelligence led operations. In the past year the force has incurred no cost associated with damage to premises, good record keeping and decision making has negated any opportunity, we have received several claims and managed to shift any costs to occupants of premises. Therefore all paperwork associated with this policy is essential and not in the bracket of bureaucratic burden."
I find it outrageous that as long as the Police keep a traceable paper trail, they can act on any allegation against a person, whether the allegation is true or false. With a search warrant they can damage property trying to gain evidence of that allegation, find no evidence and walk away leaving that person with a large bill for the damage. They can then defend themselves against any claim for compensation because they can prove that they have acted lawfully and followed proper procedure.
The person that the allegations are made against cannot defend themselves because the Police do not have to disclose what those allegations are. It seem that, even though the allegation where not proven by a search, the allegation still stands because there was enough evidence of criminality for a justice of the peace to grant a search warrant.