There are two aspects to your question. One is in relation to what's referred to as “dual charging”: The police arrive, it seems that both people have engaged in violence, and both get charged. The brief you're referring to suggests that this is because there is no flexibility, so the police have to charge that way. This is something that is not affected as much by the Criminal Code amendments themselves, but is a matter that is often addressed by prosecution policies. It's a phenomenon that prosecution officers are aware of and have policies to address. It's dealt with differently in different jurisdictions.
In relation to your question about a reverse onus in cases of intimate partner violence, this is partially addressed in the charter statement. The rationale there explains its purpose in terms of the constitutionality of it. A reverse onus in bail departs from the general approach in bail. It presumes that bail should be denied and that the accused should be detained pending trial. It requires the accused to demonstrate, on a balance of probabilities, why he or she should be released pending trial, with regard for the statutory grounds for pretrial detention: flight risk, public safety, and public confidence in the administration of justice.
There are other existing reverse onuses in the bail provisions in the Criminal Code. In terms of why the government is proposing to amend the code and add a reverse onus in the case of intimate partner violence, first of all, by restricting it to cases where the offender has a previous conviction, it's curtailing it a bit so that it would apply to the most serious cases, to the offenders who have been convicted of this type of conduct and are again before the court, allegedly having done it again. As a group, these individuals have been found to pose an elevated risk of violence, escalating the risk of reoffending toward their intimate partners. Often, when charges are laid, it can be a very volatile time in a relationship, when an intimate partner can be at greater risk. This is being proposed to increase safety in those types of situations at these very charged moments in time.